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PDBsum entry 3vx0

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Hydrolase PDB id
3vx0
Jmol
Contents
Protein chain
475 a.a.
Ligands
NAG
Metals
_CA
_GD ×6
Waters ×600
HEADER    HYDROLASE                               06-SEP-12   3VX0
TITLE     CRYSTAL STRUCTURE OF ALPHA-AMYLASE FROM ASPERGILLUS ORYZAE
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: ALPHA-AMYLASE A TYPE-1/2;
COMPND   3 CHAIN: A;
COMPND   4 SYNONYM: 1,4-ALPHA-D-GLUCAN GLUCANOHYDROLASE, TAKA-AMYLASE A, TAA;
COMPND   5 EC: 3.2.1.1
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: ASPERGILLUS ORYZAE;
SOURCE   3 ORGANISM_COMMON: YELLOW KOJI MOLD;
SOURCE   4 ORGANISM_TAXID: 510516;
SOURCE   5 STRAIN: ATCC 42149 / RIB 40
KEYWDS    HYDROLASE
EXPDTA    X-RAY DIFFRACTION
AUTHOR    M.SUGAHARA
REVDAT   1   11-SEP-13 3VX0    0
JRNL        AUTH   M.SUGAHARA
JRNL        TITL   CRYSTAL STRUCTURE OF ALPHA-AMYLASE FROM ASPERGILLUS ORYZAE
JRNL        REF    TO BE PUBLISHED
JRNL        REFN
REMARK   2
REMARK   2 RESOLUTION.    1.50 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : CNS 1.1
REMARK   3   AUTHORS     : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-
REMARK   3               : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,
REMARK   3               : READ,RICE,SIMONSON,WARREN
REMARK   3
REMARK   3  REFINEMENT TARGET : ENGH & HUBER
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 18.97
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000
REMARK   3   DATA CUTOFF HIGH         (ABS(F)) : NULL
REMARK   3   DATA CUTOFF LOW          (ABS(F)) : NULL
REMARK   3   COMPLETENESS (WORKING+TEST)   (%) : NULL
REMARK   3   NUMBER OF REFLECTIONS             : 66257
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT.
REMARK   3   CROSS-VALIDATION METHOD          : THROUGHOUT
REMARK   3   FREE R VALUE TEST SET SELECTION  : RANDOM
REMARK   3   R VALUE            (WORKING SET) : 0.192
REMARK   3   FREE R VALUE                     : 0.199
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : NULL
REMARK   3   FREE R VALUE TEST SET COUNT      : 3336
REMARK   3   ESTIMATED ERROR OF FREE R VALUE  : NULL
REMARK   3
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.
REMARK   3   TOTAL NUMBER OF BINS USED           : NULL
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : 1.50
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 1.55
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 93.10
REMARK   3   REFLECTIONS IN BIN    (WORKING SET) : NULL
REMARK   3   BIN R VALUE           (WORKING SET) : 0.2460
REMARK   3   BIN FREE R VALUE                    : 0.2590
REMARK   3   BIN FREE R VALUE TEST SET SIZE  (%) : NULL
REMARK   3   BIN FREE R VALUE TEST SET COUNT     : 333
REMARK   3   ESTIMATED ERROR OF BIN FREE R VALUE : 0.014
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            : 3680
REMARK   3   NUCLEIC ACID ATOMS       : 0
REMARK   3   HETEROGEN ATOMS          : 21
REMARK   3   SOLVENT ATOMS            : 600
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : 14.68
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 18.50
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : 0.48000
REMARK   3    B22 (A**2) : -0.97000
REMARK   3    B33 (A**2) : 0.49000
REMARK   3    B12 (A**2) : 0.00000
REMARK   3    B13 (A**2) : 0.00000
REMARK   3    B23 (A**2) : 0.00000
REMARK   3
REMARK   3  ESTIMATED COORDINATE ERROR.
REMARK   3   ESD FROM LUZZATI PLOT        (A) : 0.17
REMARK   3   ESD FROM SIGMAA              (A) : 0.14
REMARK   3   LOW RESOLUTION CUTOFF        (A) : 5.00
REMARK   3
REMARK   3  CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK   3   ESD FROM C-V LUZZATI PLOT    (A) : 0.18
REMARK   3   ESD FROM C-V SIGMAA          (A) : 0.16
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.
REMARK   3   BOND LENGTHS                 (A) : 0.009
REMARK   3   BOND ANGLES            (DEGREES) : 1.50
REMARK   3   DIHEDRAL ANGLES        (DEGREES) : NULL
REMARK   3   IMPROPER ANGLES        (DEGREES) : NULL
REMARK   3
REMARK   3  ISOTROPIC THERMAL MODEL : NULL
REMARK   3
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.    RMS    SIGMA
REMARK   3   MAIN-CHAIN BOND              (A**2) : NULL  ; NULL
REMARK   3   MAIN-CHAIN ANGLE             (A**2) : NULL  ; NULL
REMARK   3   SIDE-CHAIN BOND              (A**2) : NULL  ; NULL
REMARK   3   SIDE-CHAIN ANGLE             (A**2) : NULL  ; NULL
REMARK   3
REMARK   3  BULK SOLVENT MODELING.
REMARK   3   METHOD USED : NULL
REMARK   3   KSOL        : NULL
REMARK   3   BSOL        : NULL
REMARK   3
REMARK   3  NCS MODEL : NULL
REMARK   3
REMARK   3  NCS RESTRAINTS.                         RMS   SIGMA/WEIGHT
REMARK   3   GROUP  1  POSITIONAL            (A) : NULL  ; NULL
REMARK   3   GROUP  1  B-FACTOR           (A**2) : NULL  ; NULL
REMARK   3
REMARK   3  PARAMETER FILE  1  : NULL
REMARK   3  TOPOLOGY FILE  1   : NULL
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: NULL
REMARK   4
REMARK   4 3VX0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-SEP-12.
REMARK 100 THE RCSB ID CODE IS RCSB095605.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 14-JUL-11
REMARK 200  TEMPERATURE           (KELVIN) : 100
REMARK 200  PH                             : 5.8
REMARK 200  NUMBER OF CRYSTALS USED        : 1
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : Y
REMARK 200  RADIATION SOURCE               : SPRING-8
REMARK 200  BEAMLINE                       : BL26B1
REMARK 200  X-RAY GENERATOR MODEL          : NULL
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.000
REMARK 200  MONOCHROMATOR                  : SI
REMARK 200  OPTICS                         : NULL
REMARK 200
REMARK 200  DETECTOR TYPE                  : IMAGE PLATE
REMARK 200  DETECTOR MANUFACTURER          : RIGAKU RAXIS V
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200  DATA SCALING SOFTWARE          : HKL-2000
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 66313
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.500
REMARK 200  RESOLUTION RANGE LOW       (A) : 20.000
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 377643.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 98.5
REMARK 200  DATA REDUNDANCY                : 5.700
REMARK 200  R MERGE                    (I) : 0.10600
REMARK 200  R SYM                      (I) : NULL
REMARK 200   FOR THE DATA SET  : 7.7000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.55
REMARK 200  COMPLETENESS FOR SHELL     (%) : 95.3
REMARK 200  DATA REDUNDANCY IN SHELL       : 5.40
REMARK 200  R MERGE FOR SHELL          (I) : 0.54100
REMARK 200  R SYM FOR SHELL            (I) : NULL
REMARK 200   FOR SHELL         : 3.600
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: CNS
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 37.68
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, CACL2, PH 5.8, OIL-
REMARK 280  MICROBATCH METHOD, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
REMARK 290
REMARK 290      SYMOP   SYMMETRY
REMARK 290     NNNMMM   OPERATOR
REMARK 290       1555   X,Y,Z
REMARK 290       2555   -X+1/2,-Y,Z+1/2
REMARK 290       3555   -X,Y+1/2,-Z+1/2
REMARK 290       4555   X+1/2,-Y+1/2,-Z
REMARK 290
REMARK 290     WHERE NNN -> OPERATOR NUMBER
REMARK 290           MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000
REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000
REMARK 290   SMTRY1   2 -1.000000  0.000000  0.000000       24.26200
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       65.12150
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       32.80950
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       65.12150
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       24.26200
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       32.80950
REMARK 290   SMTRY3   4  0.000000  0.000000 -1.000000        0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000
REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465   M RES C SSSEQI
REMARK 465     SER A   476
REMARK 465     SER A   477
REMARK 465     SER A   478
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI           DISTANCE
REMARK 500   O    HOH A  1604     O    HOH A  1684              1.84
REMARK 500   OE1  GLU A    92     O    HOH A  1270              1.96
REMARK 500   O    HOH A  1585     O    HOH A  1634              2.05
REMARK 500   O    HOH A  1445     O    HOH A  1650              2.15
REMARK 500   OE1  GLU A   357     O    HOH A  1605              2.15
REMARK 500   O    HOH A  1144     O    HOH A  1364              2.16
REMARK 500   O    HOH A  1691     O    HOH A  1693              2.17
REMARK 500   O    HOH A  1545     O    HOH A  1648              2.19
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT.  AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500.  ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI  SSYMOP   DISTANCE
REMARK 500   OE1  GLU A   156     O    HOH A  1614     3655     1.87
REMARK 500   OD2  ASP A   448     O    HOH A  1605     4565     2.10
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500  M RES CSSEQI ATM1   RES CSSEQI ATM2   DEVIATION
REMARK 500    TRP A 216   NE1   TRP A 216   CE2     0.127
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500  M RES CSSEQI        PSI       PHI
REMARK 500    ALA A  78       46.76    -88.63
REMARK 500    GLN A  85      -33.52   -136.54
REMARK 500    SER A 141       41.09    -87.61
REMARK 500    ASP A 168     -155.34   -152.47
REMARK 500    ALA A 329      124.13    -38.94
REMARK 500    ASP A 340      129.08    -35.96
REMARK 500    ASP A 390     -159.30   -148.94
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY
REMARK 500
REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY
REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER
REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 500 I=INSERTION CODE).
REMARK 500
REMARK 500  M RES CSSEQI        ANGLE
REMARK 500    ALA A   1         10.61
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525  M RES CSSEQI
REMARK 525    HOH A1462        DISTANCE =  5.10 ANGSTROMS
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL
REMARK 620                              GD A1007  GD
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH A1686   O
REMARK 620 2 ASP A 206   OD1 175.6
REMARK 620 3 HOH A1685   O   101.1  83.2
REMARK 620 4 GLU A 230   OE1  94.8  80.9 164.1
REMARK 620 5 HOH A1124   O   100.0  79.9  80.0  97.2
REMARK 620 6 GLU A 230   OE2  57.6 118.2 146.1  46.0  78.7
REMARK 620 N                    1     2     3     4     5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL
REMARK 620                              GD A1002  GD
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH A1678   O
REMARK 620 2 ASP A 235   OD2  71.0
REMARK 620 3 HOH A1677   O    66.7 137.4
REMARK 620 4 HOH A1676   O   156.5  85.5 136.8
REMARK 620 5 ASP A 233   OD2 111.1 118.3  73.8  80.6
REMARK 620 6 ASP A 233   OD1  80.6  71.5  96.0  93.2  50.0
REMARK 620 N                    1     2     3     4     5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL
REMARK 620                              GD A1004  GD
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH A1680   O
REMARK 620 2 HOH A1682   O    83.5
REMARK 620 3 HOH A1679   O    72.5  62.0
REMARK 620 4 ASP A 282   OD1  79.8 137.8  76.0
REMARK 620 5 HOH A1681   O   143.8  85.3  71.8  85.8
REMARK 620 6 SER A 281   OG  130.2 146.1 125.3  64.5  69.3
REMARK 620 7 HOH A1670   O    79.2 144.0 138.3  69.3 126.1  56.9
REMARK 620 N                    1     2     3     4     5     6
REMARK 620
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL
REMARK 620                              GD A1006  GD
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH A1691   O
REMARK 620 2 HOH A1688   O    68.2
REMARK 620 3 HOH A1693   O    56.9  95.1
REMARK 620 4 HOH A1690   O   143.1  79.2 146.3
REMARK 620 5 HOH A1689   O   126.3 154.1  80.3  90.5
REMARK 620 6 ASP A  47   OD2 117.8 122.3 138.5  65.9  72.9
REMARK 620 7 HOH A1687   O   111.2  73.8  72.5  74.1  80.5 131.0
REMARK 620 8 ASP A  47   OD1  79.8  73.5 136.1  74.5 126.8  54.2 138.0
REMARK 620 9 HOH A1692   O    60.9 128.7  62.6 144.2  71.7  79.0 130.0  91.3
REMARK 620 N                    1     2     3     4     5     6     7     8
REMARK 620
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL
REMARK 620                              GD A1005  GD
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH A1684   O
REMARK 620 2 HOH A1683   O   158.3
REMARK 620 3 ASP A  50   OD1  69.2 127.1
REMARK 620 4 ASP A  50   OD2  97.5 104.2  49.4
REMARK 620 5 HOH A1444   O    99.1  68.3  92.9 128.4
REMARK 620 6 HOH A1698   O   108.1  85.5  97.5  49.8 152.8
REMARK 620 7 HOH A1591   O    58.7 127.5  90.8  71.6 154.2  51.0
REMARK 620 N                    1     2     3     4     5     6
REMARK 620
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL
REMARK 620                              CA A1008  CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASN A 121   OD1
REMARK 620 2 HIS A 210   O    76.6
REMARK 620 3 HOH A1160   O   115.2  81.7
REMARK 620 4 GLU A 162   O   155.2  80.4  69.9
REMARK 620 5 HOH A1154   O    71.9 120.8  69.0 129.3
REMARK 620 6 ASP A 175   OD2 121.8 159.4  96.5  79.8  76.8
REMARK 620 7 HOH A1206   O    88.7  81.0 146.1  78.6 144.4  89.7
REMARK 620 8 ASP A 175   OD1  76.1 138.8 138.3 117.4  78.3  50.1  68.1
REMARK 620 N                    1     2     3     4     5     6     7
REMARK 620
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL
REMARK 620                              GD A1003  GD
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 233   OD2
REMARK 620 2 HOH A1676   O    77.8
REMARK 620 3 HOH A1677   O    69.3 118.6
REMARK 620 4 GLU A 156   OE1 167.1  93.7 123.6
REMARK 620 5 HOH A1209   O    65.4 119.3  92.0 111.9
REMARK 620 N                    1     2     3     4
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GD A 1002
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GD A 1003
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GD A 1004
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GD A 1005
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GD A 1006
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GD A 1007
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1008
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR MONO-SACCHARIDE NAG A1001 BOUND
REMARK 800  TO ASN A 197
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3VX1   RELATED DB: PDB
DBREF  3VX0 A    1   478  UNP    P0C1B3   AMYA1_ASPOR     22    499
SEQRES   1 A  478  ALA THR PRO ALA ASP TRP ARG SER GLN SER ILE TYR PHE
SEQRES   2 A  478  LEU LEU THR ASP ARG PHE ALA ARG THR ASP GLY SER THR
SEQRES   3 A  478  THR ALA THR CYS ASN THR ALA ASP GLN LYS TYR CYS GLY
SEQRES   4 A  478  GLY THR TRP GLN GLY ILE ILE ASP LYS LEU ASP TYR ILE
SEQRES   5 A  478  GLN GLY MET GLY PHE THR ALA ILE TRP ILE THR PRO VAL
SEQRES   6 A  478  THR ALA GLN LEU PRO GLN THR THR ALA TYR GLY ASP ALA
SEQRES   7 A  478  TYR HIS GLY TYR TRP GLN GLN ASP ILE TYR SER LEU ASN
SEQRES   8 A  478  GLU ASN TYR GLY THR ALA ASP ASP LEU LYS ALA LEU SER
SEQRES   9 A  478  SER ALA LEU HIS GLU ARG GLY MET TYR LEU MET VAL ASP
SEQRES  10 A  478  VAL VAL ALA ASN HIS MET GLY TYR ASP GLY ALA GLY SER
SEQRES  11 A  478  SER VAL ASP TYR SER VAL PHE LYS PRO PHE SER SER GLN
SEQRES  12 A  478  ASP TYR PHE HIS PRO PHE CYS PHE ILE GLN ASN TYR GLU
SEQRES  13 A  478  ASP GLN THR GLN VAL GLU ASP CYS TRP LEU GLY ASP ASN
SEQRES  14 A  478  THR VAL SER LEU PRO ASP LEU ASP THR THR LYS ASP VAL
SEQRES  15 A  478  VAL LYS ASN GLU TRP TYR ASP TRP VAL GLY SER LEU VAL
SEQRES  16 A  478  SER ASN TYR SER ILE ASP GLY LEU ARG ILE ASP THR VAL
SEQRES  17 A  478  LYS HIS VAL GLN LYS ASP PHE TRP PRO GLY TYR ASN LYS
SEQRES  18 A  478  ALA ALA GLY VAL TYR CYS ILE GLY GLU VAL LEU ASP GLY
SEQRES  19 A  478  ASP PRO ALA TYR THR CYS PRO TYR GLN ASN VAL MET ASP
SEQRES  20 A  478  GLY VAL LEU ASN TYR PRO ILE TYR TYR PRO LEU LEU ASN
SEQRES  21 A  478  ALA PHE LYS SER THR SER GLY SER MET ASP ASP LEU TYR
SEQRES  22 A  478  ASN MET ILE ASN THR VAL LYS SER ASP CYS PRO ASP SER
SEQRES  23 A  478  THR LEU LEU GLY THR PHE VAL GLU ASN HIS ASP ASN PRO
SEQRES  24 A  478  ARG PHE ALA SER TYR THR ASN ASP ILE ALA LEU ALA LYS
SEQRES  25 A  478  ASN VAL ALA ALA PHE ILE ILE LEU ASN ASP GLY ILE PRO
SEQRES  26 A  478  ILE ILE TYR ALA GLY GLN GLU GLN HIS TYR ALA GLY GLY
SEQRES  27 A  478  ASN ASP PRO ALA ASN ARG GLU ALA THR TRP LEU SER GLY
SEQRES  28 A  478  TYR PRO THR ASP SER GLU LEU TYR LYS LEU ILE ALA SER
SEQRES  29 A  478  ALA ASN ALA ILE ARG ASN TYR ALA ILE SER LYS ASP THR
SEQRES  30 A  478  GLY PHE VAL THR TYR LYS ASN TRP PRO ILE TYR LYS ASP
SEQRES  31 A  478  ASP THR THR ILE ALA MET ARG LYS GLY THR ASP GLY SER
SEQRES  32 A  478  GLN ILE VAL THR ILE LEU SER ASN LYS GLY ALA SER GLY
SEQRES  33 A  478  ASP SER TYR THR LEU SER LEU SER GLY ALA GLY TYR THR
SEQRES  34 A  478  ALA GLY GLN GLN LEU THR GLU VAL ILE GLY CYS THR THR
SEQRES  35 A  478  VAL THR VAL GLY SER ASP GLY ASN VAL PRO VAL PRO MET
SEQRES  36 A  478  ALA GLY GLY LEU PRO ARG VAL LEU TYR PRO THR GLU LYS
SEQRES  37 A  478  LEU ALA GLY SER LYS ILE CYS SER SER SER
MODRES 3VX0 ASN A  197  ASN  GLYCOSYLATION SITE
HET    NAG  A1001      14
HET     GD  A1002       1
HET     GD  A1003       1
HET     GD  A1004       1
HET     GD  A1005       1
HET     GD  A1006       1
HET     GD  A1007       1
HET     CA  A1008       1
HETNAM     NAG N-ACETYL-D-GLUCOSAMINE
HETNAM      GD GADOLINIUM ATOM
HETNAM      CA CALCIUM ION
FORMUL   2  NAG    C8 H15 N O6
FORMUL   3   GD    6(GD)
FORMUL   9   CA    CA 2+
FORMUL  10  HOH   *600(H2 O)
HELIX    1   1 THR A    2  ARG A    7  1                                   6
HELIX    2   2 LEU A   15  ALA A   20  1                                   6
HELIX    3   3 ASN A   31  GLN A   35  5                                   5
HELIX    4   4 THR A   41  LYS A   48  1                                   8
HELIX    5   5 LYS A   48  GLY A   54  1                                   7
HELIX    6   6 THR A   96  ARG A  110  1                                  15
HELIX    7   7 ALA A  128  VAL A  132  5                                   5
HELIX    8   8 ASP A  133  PHE A  137  5                                   5
HELIX    9   9 SER A  142  PHE A  146  5                                   5
HELIX   10  10 ASP A  157  CYS A  164  1                                   8
HELIX   11  11 LYS A  180  SER A  199  1                                  20
HELIX   12  12 THR A  207  VAL A  211  5                                   5
HELIX   13  13 GLN A  212  ASP A  214  5                                   3
HELIX   14  14 PHE A  215  GLY A  224  1                                  10
HELIX   15  15 ASP A  235  CYS A  240  1                                   6
HELIX   16  16 PRO A  241  VAL A  245  5                                   5
HELIX   17  17 ASN A  251  LYS A  263  1                                  13
HELIX   18  18 SER A  268  CYS A  283  1                                  16
HELIX   19  19 ASP A  285  LEU A  288  5                                   4
HELIX   20  20 ARG A  300  THR A  305  1                                   6
HELIX   21  21 ASP A  307  ASN A  321  1                                  15
HELIX   22  22 GLY A  330  HIS A  334  5                                   5
HELIX   23  23 ALA A  346  GLY A  351  5                                   6
HELIX   24  24 SER A  356  ASP A  376  1                                  21
HELIX   25  25 GLU A  467  ALA A  470  5                                   4
SHEET    1   A 8 GLY A 248  VAL A 249  0
SHEET    2   A 8 TYR A 226  GLY A 229  1  N  GLY A 229   O  GLY A 248
SHEET    3   A 8 GLY A 202  ILE A 205  1  N  ILE A 205   O  ILE A 228
SHEET    4   A 8 TYR A 113  VAL A 118  1  N  VAL A 118   O  ARG A 204
SHEET    5   A 8 ALA A  59  ILE A  62  1  N  ILE A  60   O  MET A 115
SHEET    6   A 8 ILE A  11  LEU A  14  1  N  LEU A  14   O  TRP A  61
SHEET    7   A 8 ILE A 324  TYR A 328  1  O  ILE A 327   N  PHE A  13
SHEET    8   A 8 GLY A 290  THR A 291  1  N  THR A 291   O  ILE A 326
SHEET    1   B 2 THR A  66  GLN A  68  0
SHEET    2   B 2 GLN A  84  LEU A  90 -1  O  GLN A  85   N  ALA A  67
SHEET    1   C 3 TYR A 125  ASP A 126  0
SHEET    2   C 3 VAL A 171  LEU A 173 -1  O  SER A 172   N  TYR A 125
SHEET    3   C 3 LEU A 166  GLY A 167 -1  N  LEU A 166   O  LEU A 173
SHEET    1   D 6 TRP A 385  LYS A 389  0
SHEET    2   D 6 THR A 393  LYS A 398 -1  O  ARG A 397   N  TRP A 385
SHEET    3   D 6 ILE A 405  SER A 410 -1  O  LEU A 409   N  ILE A 394
SHEET    4   D 6 ARG A 461  PRO A 465 -1  O  LEU A 463   N  VAL A 406
SHEET    5   D 6 GLN A 433  GLU A 436 -1  N  THR A 435   O  TYR A 464
SHEET    6   D 6 THR A 441  THR A 444 -1  O  THR A 441   N  GLU A 436
SHEET    1   E 2 TYR A 419  LEU A 423  0
SHEET    2   E 2 VAL A 451  MET A 455 -1  O  MET A 455   N  TYR A 419
SSBOND   1 CYS A   30    CYS A   38                          1555   1555  2.02
SSBOND   2 CYS A  150    CYS A  164                          1555   1555  2.02
SSBOND   3 CYS A  240    CYS A  283                          1555   1555  2.03
SSBOND   4 CYS A  440    CYS A  475                          1555   1555  2.02
LINK         ND2 ASN A 197                 C1  NAG A1001     1555   1555  1.43
LINK        GD    GD A1007                 O   HOH A1686     1555   1555  2.12
LINK        GD    GD A1002                 O   HOH A1678     1555   1555  2.21
LINK        GD    GD A1004                 O   HOH A1680     1555   1555  2.22
LINK        GD    GD A1006                 O   HOH A1691     1555   1555  2.26
LINK        GD    GD A1006                 O   HOH A1688     1555   1555  2.27
LINK        GD    GD A1004                 O   HOH A1682     1555   1555  2.29
LINK        GD    GD A1006                 O   HOH A1693     1555   1555  2.30
LINK         OD2 ASP A 235                GD    GD A1002     1555   1555  2.32
LINK        GD    GD A1006                 O   HOH A1690     1555   1555  2.32
LINK        GD    GD A1006                 O   HOH A1689     1555   1555  2.34
LINK        GD    GD A1005                 O   HOH A1684     1555   1555  2.35
LINK        GD    GD A1002                 O   HOH A1677     1555   1555  2.36
LINK         OD1 ASP A 206                GD    GD A1007     1555   1555  2.36
LINK         OD2 ASP A  47                GD    GD A1006     1555   1555  2.36
LINK        GD    GD A1006                 O   HOH A1687     1555   1555  2.36
LINK        GD    GD A1002                 O   HOH A1676     1555   1555  2.37
LINK        GD    GD A1004                 O   HOH A1679     1555   1555  2.40
LINK        GD    GD A1007                 O   HOH A1685     1555   1555  2.41
LINK         OD1 ASN A 121                CA    CA A1008     1555   1555  2.42
LINK         OE1 GLU A 230                GD    GD A1007     1555   1555  2.45
LINK         OD1 ASP A 282                GD    GD A1004     1555   1555  2.45
LINK         OD1 ASP A  47                GD    GD A1006     1555   1555  2.46
LINK         OD2 ASP A 233                GD    GD A1002     1555   1555  2.46
LINK         O   HIS A 210                CA    CA A1008     1555   1555  2.47
LINK         OD2 ASP A 233                GD    GD A1003     1555   1555  2.48
LINK        GD    GD A1005                 O   HOH A1683     1555   1555  2.50
LINK        GD    GD A1003                 O   HOH A1676     1555   1555  2.51
LINK        GD    GD A1004                 O   HOH A1681     1555   1555  2.51
LINK        GD    GD A1006                 O   HOH A1692     1555   1555  2.52
LINK        GD    GD A1007                 O   HOH A1124     1555   1555  2.53
LINK        CA    CA A1008                 O   HOH A1160     1555   1555  2.53
LINK         O   GLU A 162                CA    CA A1008     1555   1555  2.55
LINK        CA    CA A1008                 O   HOH A1154     1555   1555  2.55
LINK         OD2 ASP A 175                CA    CA A1008     1555   1555  2.57
LINK        CA    CA A1008                 O   HOH A1206     1555   1555  2.57
LINK        GD    GD A1003                 O   HOH A1677     1555   1555  2.61
LINK         OD1 ASP A  50                GD    GD A1005     1555   1555  2.62
LINK         OD2 ASP A  50                GD    GD A1005     1555   1555  2.64
LINK        GD    GD A1005                 O   HOH A1444     1555   1555  2.65
LINK         OD1 ASP A 233                GD    GD A1002     1555   1555  2.66
LINK         OD1 ASP A 175                CA    CA A1008     1555   1555  2.66
LINK         OG  SER A 281                GD    GD A1004     1555   1555  2.75
LINK        GD    GD A1005                 O   HOH A1698     1555   1555  2.91
LINK        GD    GD A1004                 O   HOH A1670     1555   1555  2.99
LINK         OE2 GLU A 230                GD    GD A1007     1555   1555  3.00
LINK        GD    GD A1005                 O   HOH A1591     1555   1555  3.04
LINK         OE1 GLU A 156                GD    GD A1003     1555   1555  3.35
LINK        GD    GD A1003                 O   HOH A1209     1555   1555  3.46
CISPEP   1 LYS A  138    PRO A  139          0         0.35
CISPEP   2 ASP A  340    PRO A  341          0        -0.44
SITE     1 AC1  7 ASP A 144  ASP A 233  ASP A 235   GD A1003
SITE     2 AC1  7 HOH A1676  HOH A1677  HOH A1678
SITE     1 AC2  6 ASP A 144  GLU A 156  ASP A 233   GD A1002
SITE     2 AC2  6 HOH A1676  HOH A1677
SITE     1 AC3  8 SER A 281  ASP A 282  ASP A 355  HOH A1670
SITE     2 AC3  8 HOH A1679  HOH A1680  HOH A1681  HOH A1682
SITE     1 AC4  7 ASP A   5  ASP A  50  HOH A1444  HOH A1591
SITE     2 AC4  7 HOH A1683  HOH A1684  HOH A1698
SITE     1 AC5  8 ASP A  47  HOH A1687  HOH A1688  HOH A1689
SITE     2 AC5  8 HOH A1690  HOH A1691  HOH A1692  HOH A1693
SITE     1 AC6  5 ASP A 206  GLU A 230  HOH A1124  HOH A1685
SITE     2 AC6  5 HOH A1686
SITE     1 AC7  7 ASN A 121  GLU A 162  ASP A 175  HIS A 210
SITE     2 AC7  7 HOH A1154  HOH A1160  HOH A1206
SITE     1 AC8  8 TYR A  88  TRP A 190  LEU A 194  ASN A 197
SITE     2 AC8  8 HOH A1110  HOH A1254  HOH A1587  HOH A1632
CRYST1   48.524   65.619  130.243  90.00  90.00  90.00 P 21 21 21    4
ORIGX1      1.000000  0.000000  0.000000        0.00000
ORIGX2      0.000000  1.000000  0.000000        0.00000
ORIGX3      0.000000  0.000000  1.000000        0.00000
SCALE1      0.020608  0.000000  0.000000        0.00000
SCALE2      0.000000  0.015239  0.000000        0.00000
SCALE3      0.000000  0.000000  0.007678        0.00000
      
PROCHECK
Go to PROCHECK summary
 References