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PDBsum entry 2xfy

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Hydrolase PDB id
2xfy
Jmol
Contents
Protein chain
486 a.a.
Ligands
ACX
EDO ×2
Waters ×817
HEADER    HYDROLASE                               28-MAY-10   2XFY
TITLE     CRYSTAL STRUCTURE OF BARLEY BETA-AMYLASE COMPLEXED WITH
TITLE    2 ALPHA-CYCLODEXTRIN
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: BETA-AMYLASE;
COMPND   3 CHAIN: A;
COMPND   4 SYNONYM: 1,4-ALPHA-D-GLUCAN MALTOHYDROLASE;
COMPND   5 EC: 3.2.1.2
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: HORDEUM VULGARE;
SOURCE   3 ORGANISM_COMMON: BARLEY;
SOURCE   4 ORGANISM_TAXID: 4513;
SOURCE   5 TISSUE: GRAIN ENDOSPERM;
SOURCE   6 OTHER_DETAILS: PROTEIN PURCHASED FROM MEGAZYME
KEYWDS    CARBOHYDRATE METABOLISM, HYDROLASE, GERMINATION
EXPDTA    X-RAY DIFFRACTION
AUTHOR    M.REJZEK,C.E.M.STEVENSON,A.M.SOUTHARD,D.STANLEY,K.DENYER,A.M.SMITH,
AUTHOR   2 M.J.NALDRETT,D.M.LAWSON,R.A.FIELD
REVDAT   2   11-JAN-12 2XFY    1       JRNL   REMARK VERSN
REVDAT   1   01-DEC-10 2XFY    0
JRNL        AUTH   M.REJZEK,C.E.M.STEVENSON,A.M.SOUTHARD,D.STANLEY,K.DENYER,
JRNL        AUTH 2 A.M.SMITH,M.J.NALDRETT,D.M.LAWSON,R.A.FIELD
JRNL        TITL   CHEMICAL GENETICS AND CEREAL STARCH METABOLISM: STRUCTURAL
JRNL        TITL 2 BASIS OF THE NON-COVALENT AND COVALENT INHIBITION OF BARLEY
JRNL        TITL 3 BETA-AMYLASE.
JRNL        REF    MOL.BIOSYST.                  V.   7   718 2011
JRNL        REFN                   ISSN 1742-206X
JRNL        PMID   21085740
JRNL        DOI    10.1039/C0MB00204F
REMARK   2
REMARK   2 RESOLUTION.    1.21 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : REFMAC 5.5.0091
REMARK   3   AUTHORS     : MURSHUDOV,VAGIN,DODSON
REMARK   3
REMARK   3    REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.207
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 25.760
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.0
REMARK   3   COMPLETENESS FOR RANGE        (%) : 98.783
REMARK   3   NUMBER OF REFLECTIONS             : 138417
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 + TEST SET) : 0.124
REMARK   3   R VALUE            (WORKING SET) : 0.1221
REMARK   3   FREE R VALUE                     : 0.1533
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.06
REMARK   3   FREE R VALUE TEST SET COUNT      : 6970
REMARK   3
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.
REMARK   3   TOTAL NUMBER OF BINS USED           : 20
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : 1.207
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 1.239
REMARK   3   REFLECTION IN BIN     (WORKING SET) : 9134
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 94.091
REMARK   3   BIN R VALUE           (WORKING SET) : 0.27
REMARK   3   BIN FREE R VALUE SET COUNT          : 499
REMARK   3   BIN FREE R VALUE                    : 0.305
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            : 4207
REMARK   3   NUCLEIC ACID ATOMS       : 0
REMARK   3   HETEROGEN ATOMS          : 74
REMARK   3   SOLVENT ATOMS            : 817
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : 9.0
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 9.3
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : -0.096
REMARK   3    B22 (A**2) : 0.199
REMARK   3    B33 (A**2) : -0.103
REMARK   3    B12 (A**2) : 0.000
REMARK   3    B13 (A**2) : 0.000
REMARK   3    B23 (A**2) : 0.000
REMARK   3
REMARK   3  ESTIMATED OVERALL COORDINATE ERROR.
REMARK   3   ESU BASED ON R VALUE                            (A): 0.037
REMARK   3   ESU BASED ON FREE R VALUE                       (A): 0.037
REMARK   3   ESU BASED ON MAXIMUM LIKELIHOOD                 (A): 0.021
REMARK   3   ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.050
REMARK   3
REMARK   3  CORRELATION COEFFICIENTS.
REMARK   3   CORRELATION COEFFICIENT FO-FC      : 0.980
REMARK   3   CORRELATION COEFFICIENT FO-FC FREE : 0.971
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES        COUNT    RMS    WEIGHT
REMARK   3   BOND LENGTHS REFINED ATOMS        (A):  4451 ; 0.016 ; 0.022
REMARK   3   BOND LENGTHS OTHERS               (A):  NULL ;  NULL ;  NULL
REMARK   3   BOND ANGLES REFINED ATOMS   (DEGREES):  6120 ; 1.671 ; 1.965
REMARK   3   BOND ANGLES OTHERS          (DEGREES):  NULL ;  NULL ;  NULL
REMARK   3   TORSION ANGLES, PERIOD 1    (DEGREES):   586 ; 6.000 ; 5.000
REMARK   3   TORSION ANGLES, PERIOD 2    (DEGREES):   233 ;37.375 ;24.034
REMARK   3   TORSION ANGLES, PERIOD 3    (DEGREES):   747 ;12.354 ;15.000
REMARK   3   TORSION ANGLES, PERIOD 4    (DEGREES):    32 ;16.028 ;15.000
REMARK   3   CHIRAL-CENTER RESTRAINTS       (A**3):   647 ; 0.110 ; 0.200
REMARK   3   GENERAL PLANES REFINED ATOMS      (A):  5059 ; 0.010 ; 0.021
REMARK   3   GENERAL PLANES OTHERS             (A):  NULL ;  NULL ;  NULL
REMARK   3   NON-BONDED CONTACTS REFINED ATOMS (A):  NULL ;  NULL ;  NULL
REMARK   3   NON-BONDED CONTACTS OTHERS        (A):  NULL ;  NULL ;  NULL
REMARK   3   NON-BONDED TORSION REFINED ATOMS  (A):  NULL ;  NULL ;  NULL
REMARK   3   NON-BONDED TORSION OTHERS         (A):  NULL ;  NULL ;  NULL
REMARK   3   H-BOND (X...Y) REFINED ATOMS      (A):  NULL ;  NULL ;  NULL
REMARK   3   H-BOND (X...Y) OTHERS             (A):  NULL ;  NULL ;  NULL
REMARK   3   POTENTIAL METAL-ION REFINED ATOMS (A):  NULL ;  NULL ;  NULL
REMARK   3   POTENTIAL METAL-ION OTHERS        (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY VDW REFINED ATOMS        (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY VDW OTHERS               (A):    44 ; 0.168 ; 0.200
REMARK   3   SYMMETRY H-BOND REFINED ATOMS     (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY H-BOND OTHERS            (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY METAL-ION REFINED ATOMS  (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY METAL-ION OTHERS         (A):  NULL ;  NULL ;  NULL
REMARK   3
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.     COUNT   RMS    WEIGHT
REMARK   3   MAIN-CHAIN BOND REFINED ATOMS  (A**2):  2601 ; 1.625 ; 1.500
REMARK   3   MAIN-CHAIN BOND OTHER ATOMS    (A**2):  1044 ; 0.747 ; 1.500
REMARK   3   MAIN-CHAIN ANGLE REFINED ATOMS (A**2):  4241 ; 2.375 ; 2.000
REMARK   3   SIDE-CHAIN BOND REFINED ATOMS  (A**2):  1850 ; 3.152 ; 3.000
REMARK   3   SIDE-CHAIN ANGLE REFINED ATOMS (A**2):  1831 ; 4.371 ; 4.500
REMARK   3
REMARK   3  ANISOTROPIC THERMAL FACTOR RESTRAINTS.   COUNT   RMS    WEIGHT
REMARK   3   RIGID-BOND RESTRAINTS          (A**2):  7540 ; 1.517 ; 3.000
REMARK   3   SPHERICITY; FREE ATOMS         (A**2):   817 ; 8.817 ; 3.000
REMARK   3   SPHERICITY; BONDED ATOMS       (A**2):  7370 ; 3.990 ; 3.000
REMARK   3
REMARK   3  NCS RESTRAINTS STATISTICS
REMARK   3   NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK   3
REMARK   3  TLS DETAILS
REMARK   3   NUMBER OF TLS GROUPS  : NULL
REMARK   3
REMARK   3  BULK SOLVENT MODELLING.
REMARK   3   METHOD USED : MASK BULK SOLVENT
REMARK   3   PARAMETERS FOR MASK CALCULATION
REMARK   3   VDW PROBE RADIUS   : 1.400
REMARK   3   ION PROBE RADIUS   : 0.800
REMARK   3   SHRINKAGE RADIUS   : 0.800
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE
REMARK   3   RIDING POSITIONS.
REMARK   4
REMARK   4 2XFY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-MAY-10.
REMARK 100 THE PDBE ID CODE IS EBI-44087.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 08-MAR-08
REMARK 200  TEMPERATURE           (KELVIN) : 100
REMARK 200  PH                             : 5.5
REMARK 200  NUMBER OF CRYSTALS USED        : 1
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : Y
REMARK 200  RADIATION SOURCE               : DIAMOND
REMARK 200  BEAMLINE                       : I02
REMARK 200  X-RAY GENERATOR MODEL          : NULL
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.9507
REMARK 200  MONOCHROMATOR                  : NULL
REMARK 200  OPTICS                         : NULL
REMARK 200
REMARK 200  DETECTOR TYPE                  : CCD
REMARK 200  DETECTOR MANUFACTURER          : ADSC
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : MOSFLM
REMARK 200  DATA SCALING SOFTWARE          : SCALA
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 139370
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.19
REMARK 200  RESOLUTION RANGE LOW       (A) : 28.09
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : -9.0
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 98.4
REMARK 200  DATA REDUNDANCY                : 5.19
REMARK 200  R MERGE                    (I) : 0.08
REMARK 200  R SYM                      (I) : NULL
REMARK 200   FOR THE DATA SET  : 6.31
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.19
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.26
REMARK 200  COMPLETENESS FOR SHELL     (%) : 90.8
REMARK 200  DATA REDUNDANCY IN SHELL       : 4.63
REMARK 200  R MERGE FOR SHELL          (I) : 0.50
REMARK 200  R SYM FOR SHELL            (I) : NULL
REMARK 200   FOR SHELL         : 1.46
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: AMORE
REMARK 200 STARTING MODEL: PDB ENTRY 1B1Y
REMARK 200
REMARK 200 REMARK: NONE
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 35.6
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS WERE GROWN AT 291 K
REMARK 280  USING THE HANGING DROP VAPOUR DIFFUSION METHOD WITH
REMARK 280  PROTEIN AT 10 MG PER ML AND A PRECIPITANT COMPRISED OF 14
REMARK 280  PERCENT PEG 3350 IN 100 MM BIS-TRIS PROPANE BUFFER AT PH
REMARK 280  5.5
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       34.42300
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       46.23600
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       35.73300
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       46.23600
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       34.42300
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       35.73300
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     MET A     1
REMARK 465     GLU A     2
REMARK 465     VAL A     3
REMARK 465     PRO A   490
REMARK 465     THR A   491
REMARK 465     GLY A   492
REMARK 465     GLY A   493
REMARK 465     MET A   494
REMARK 465     GLY A   495
REMARK 465     GLY A   496
REMARK 465     GLN A   497
REMARK 465     ALA A   498
REMARK 465     GLU A   499
REMARK 465     GLY A   500
REMARK 465     PRO A   501
REMARK 465     THR A   502
REMARK 465     CYS A   503
REMARK 465     GLY A   504
REMARK 465     MET A   505
REMARK 465     GLY A   506
REMARK 465     GLY A   507
REMARK 465     GLN A   508
REMARK 465     VAL A   509
REMARK 465     LYS A   510
REMARK 465     GLY A   511
REMARK 465     PRO A   512
REMARK 465     THR A   513
REMARK 465     GLY A   514
REMARK 465     GLY A   515
REMARK 465     MET A   516
REMARK 465     GLY A   517
REMARK 465     GLY A   518
REMARK 465     GLN A   519
REMARK 465     ALA A   520
REMARK 465     GLU A   521
REMARK 465     ASP A   522
REMARK 465     PRO A   523
REMARK 465     THR A   524
REMARK 465     SER A   525
REMARK 465     GLY A   526
REMARK 465     ILE A   527
REMARK 465     GLY A   528
REMARK 465     GLY A   529
REMARK 465     GLU A   530
REMARK 465     LEU A   531
REMARK 465     PRO A   532
REMARK 465     ALA A   533
REMARK 465     THR A   534
REMARK 465     MET A   535
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470   M RES CSSEQI  ATOMS
REMARK 470     ARG A  26    NE   CZ   NH1  NH2
REMARK 470     GLU A 482    CD   OE1  OE2
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  2099     O    HOH A  2416              1.61
REMARK 500   O    HOH A  2634     O    HOH A  2635              1.91
REMARK 500   O    HOH A  2566     O    HOH A  2568              1.92
REMARK 500   O    HOH A  2720     O    HOH A  2730              2.02
REMARK 500   O    HOH A  2291     O    HOH A  2645              2.07
REMARK 500   O    HOH A  2530     O    HOH A  2767              2.08
REMARK 500   O    HOH A  2212     O    HOH A  2767              2.11
REMARK 500   OH   TYR A   207     O    HOH A  2418              2.11
REMARK 500   O    HOH A  2208     O    HOH A  2521              2.15
REMARK 500   O    HOH A  2279     O    HOH A  2634              2.15
REMARK 500   O    HOH A  2374     O    HOH A  2786              2.18
REMARK 500   O    HOH A  2103     O    HOH A  2200              2.18
REMARK 500   O    HOH A  2224     O    HOH A  2350              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   OG   SER A   404     O3A  ACX A   600     3655     2.16
REMARK 500   O    HOH A  2072     O    HOH A  2369     4556     1.81
REMARK 500   O    HOH A  2452     O    HOH A  2568     4455     2.14
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
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   ATM2   ATM3
REMARK 500    MET A  49   CG  -  SD  -  CE  ANGL. DEV. = -16.5 DEGREES
REMARK 500    ARG A 370   NE  -  CZ  -  NH1 ANGL. DEV. =   3.3 DEGREES
REMARK 500    ARG A 445   NE  -  CZ  -  NH2 ANGL. DEV. =  -3.7 DEGREES
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    PHE A  90       37.33    -90.04
REMARK 500    PHE A 143       79.87   -113.42
REMARK 500    PRO A 199       50.60   -102.92
REMARK 500    ILE A 205       59.14   -113.28
REMARK 500    PHE A 339     -168.99   -106.71
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: PLANAR GROUPS
REMARK 500
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
REMARK 500 AN RMSD GREATER THAN THIS VALUE
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500  M RES CSSEQI        RMS     TYPE
REMARK 500    ARG A 242         0.08    SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 600
REMARK 600 HETEROGEN
REMARK 600 1,2-ETHANEDIOL (EDO): PRESENT AT 20 PERCENT IN THE
REMARK 600  CRYOPROTECTANT
REMARK 600 ALPHA-CYCLODEXTRIN (CYCLOHEXA-AMYLOSE) (ACX): SOAKED INTO
REMARK 600  CRYSTALS AT 10 MM FOR 24 HOURS
REMARK 700
REMARK 700 SHEET
REMARK 700 DETERMINATION METHOD: DSSP
REMARK 700 THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS
REMARK 700 BELOW IS ACTUALLY AN  8-STRANDED BARREL THIS IS REPRESENTED BY
REMARK 700 A  9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS
REMARK 700 ARE IDENTICAL.
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACX A 600
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1490
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1491
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2XG9   RELATED DB: PDB
REMARK 900  CRYSTAL STRUCTURE OF BARLEY BETA-AMYLASE
REMARK 900  COMPLEXED WITH 4-O-ALPHA-D-
REMARK 900  GLUCOPYRANOSYLMORANOLINE
REMARK 900 RELATED ID: 2XGB   RELATED DB: PDB
REMARK 900  CRYSTAL STRUCTURE OF BARLEY BETA-AMYLASE
REMARK 900  COMPLEXED WITH 2,3-EPOXYPROPYL-ALPHA-D-
REMARK 900  GLUCOPYRANOSIDE
REMARK 900 RELATED ID: 2XFF   RELATED DB: PDB
REMARK 900  CRYSTAL STRUCTURE OF BARLEY BETA-AMYLASE
REMARK 900  COMPLEXED WITH ACARBOSE
REMARK 900 RELATED ID: 2XGI   RELATED DB: PDB
REMARK 900  CRYSTAL STRUCTURE OF BARLEY BETA-AMYLASE
REMARK 900  COMPLEXED WITH 3,4-EPOXYBUTYL ALPHA-D-
REMARK 900  GLUCOPYRANOSIDE
REMARK 900 RELATED ID: 1B1Y   RELATED DB: PDB
REMARK 900  SEVENFOLD MUTANT OF BARLEY BETA-AMYLASE
REMARK 900 RELATED ID: 2XFR   RELATED DB: PDB
REMARK 900  TOWARDS THE DISSECTION OF CEREAL STARCH
REMARK 900  METABOLISM THROUGH CHEMICAL GENETICS: STRUCTURAL
REMARK 900   BASIS OF THE NON-COVALENT AND COVALENT
REMARK 900  INHIBITION OF BARLEY BETA-AMYLASE
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 PROTEIN ISOLATED FROM NATURAL SOURCE BUT SEQUENCE DIFFERS
REMARK 999 AT 3 POSITIONS TO UNIPROTKB DATABASE ENTRY P16098. THESE
REMARK 999 CHANGES WERE IDENTIFIED FROM ELECTRON DENSITY MAPS. AUTHOR
REMARK 999 SUGGESTS THESE ARE NATURAL VARIANTS
DBREF  2XFY A    1   535  UNP    P16098   AMYB_HORVU       1    535
SEQADV 2XFY GLU A  165  UNP  P16098    ASP   165 SEE REMARK 999
SEQADV 2XFY SER A  347  UNP  P16098    LEU   347 SEE REMARK 999
SEQADV 2XFY ALA A  430  UNP  P16098    VAL   430 SEE REMARK 999
SEQRES   1 A  535  MET GLU VAL ASN VAL LYS GLY ASN TYR VAL GLN VAL TYR
SEQRES   2 A  535  VAL MET LEU PRO LEU ASP ALA VAL SER VAL ASN ASN ARG
SEQRES   3 A  535  PHE GLU LYS GLY ASP GLU LEU ARG ALA GLN LEU ARG LYS
SEQRES   4 A  535  LEU VAL GLU ALA GLY VAL ASP GLY VAL MET VAL ASP VAL
SEQRES   5 A  535  TRP TRP GLY LEU VAL GLU GLY LYS GLY PRO LYS ALA TYR
SEQRES   6 A  535  ASP TRP SER ALA TYR LYS GLN LEU PHE GLU LEU VAL GLN
SEQRES   7 A  535  LYS ALA GLY LEU LYS LEU GLN ALA ILE MET SER PHE HIS
SEQRES   8 A  535  GLN CYS GLY GLY ASN VAL GLY ASP ALA VAL ASN ILE PRO
SEQRES   9 A  535  ILE PRO GLN TRP VAL ARG ASP VAL GLY THR ARG ASP PRO
SEQRES  10 A  535  ASP ILE PHE TYR THR ASP GLY HIS GLY THR ARG ASN ILE
SEQRES  11 A  535  GLU TYR LEU THR LEU GLY VAL ASP ASN GLN PRO LEU PHE
SEQRES  12 A  535  HIS GLY ARG SER ALA VAL GLN MET TYR ALA ASP TYR MET
SEQRES  13 A  535  THR SER PHE ARG GLU ASN MET LYS GLU PHE LEU ASP ALA
SEQRES  14 A  535  GLY VAL ILE VAL ASP ILE GLU VAL GLY LEU GLY PRO ALA
SEQRES  15 A  535  GLY GLU MET ARG TYR PRO SER TYR PRO GLN SER HIS GLY
SEQRES  16 A  535  TRP SER PHE PRO GLY ILE GLY GLU PHE ILE CYS TYR ASP
SEQRES  17 A  535  LYS TYR LEU GLN ALA ASP PHE LYS ALA ALA ALA ALA ALA
SEQRES  18 A  535  VAL GLY HIS PRO GLU TRP GLU PHE PRO ASN ASP VAL GLY
SEQRES  19 A  535  GLN TYR ASN ASP THR PRO GLU ARG THR GLN PHE PHE ARG
SEQRES  20 A  535  ASP ASN GLY THR TYR LEU SER GLU LYS GLY ARG PHE PHE
SEQRES  21 A  535  LEU ALA TRP TYR SER ASN ASN LEU ILE LYS HIS GLY ASP
SEQRES  22 A  535  ARG ILE LEU ASP GLU ALA ASN LYS VAL PHE LEU GLY TYR
SEQRES  23 A  535  LYS VAL GLN LEU ALA ILE LYS ILE SER GLY ILE HIS TRP
SEQRES  24 A  535  TRP TYR LYS VAL PRO SER HIS ALA ALA GLU LEU THR ALA
SEQRES  25 A  535  GLY TYR TYR ASN LEU HIS ASP ARG ASP GLY TYR ARG THR
SEQRES  26 A  535  ILE ALA ARG MET LEU LYS ARG HIS ARG ALA SER ILE ASN
SEQRES  27 A  535  PHE THR CYS ALA GLU MET ARG ASP SER GLU GLN SER SER
SEQRES  28 A  535  GLN ALA MET SER ALA PRO GLU GLU LEU VAL GLN GLN VAL
SEQRES  29 A  535  LEU SER ALA GLY TRP ARG GLU GLY LEU ASN VAL ALA CYS
SEQRES  30 A  535  GLU ASN ALA LEU PRO ARG TYR ASP PRO THR ALA TYR ASN
SEQRES  31 A  535  THR ILE LEU ARG ASN ALA ARG PRO HIS GLY ILE ASN GLN
SEQRES  32 A  535  SER GLY PRO PRO GLU HIS LYS LEU PHE GLY PHE THR TYR
SEQRES  33 A  535  LEU ARG LEU SER ASN GLN LEU VAL GLU GLY GLN ASN TYR
SEQRES  34 A  535  ALA ASN PHE LYS THR PHE VAL ASP ARG MET HIS ALA ASN
SEQRES  35 A  535  LEU PRO ARG ASP PRO TYR VAL ASP PRO MET ALA PRO LEU
SEQRES  36 A  535  PRO ARG SER GLY PRO GLU ILE SER ILE GLU MET ILE LEU
SEQRES  37 A  535  GLN ALA ALA GLN PRO LYS LEU GLN PRO PHE PRO PHE GLN
SEQRES  38 A  535  GLU HIS THR ASP LEU PRO VAL GLY PRO THR GLY GLY MET
SEQRES  39 A  535  GLY GLY GLN ALA GLU GLY PRO THR CYS GLY MET GLY GLY
SEQRES  40 A  535  GLN VAL LYS GLY PRO THR GLY GLY MET GLY GLY GLN ALA
SEQRES  41 A  535  GLU ASP PRO THR SER GLY ILE GLY GLY GLU LEU PRO ALA
SEQRES  42 A  535  THR MET
HET    ACX  A 600      66
HET    EDO  A1490       4
HET    EDO  A1491       4
HETNAM     ACX ALPHA-CYCLODEXTRIN (CYCLOHEXA-AMYLOSE)
HETNAM     EDO 1,2-ETHANEDIOL
HETSYN     EDO ETHYLENE GLYCOL
FORMUL   2  ACX    C36 H60 O30
FORMUL   3  EDO    2(C2 H6 O2)
FORMUL   4  HOH   *817(H2 O)
HELIX    1   1 VAL A    5  TYR A    9  5                                   5
HELIX    2   2 LYS A   29  ALA A   43  1                                  15
HELIX    3   3 TRP A   54  GLU A   58  1                                   5
HELIX    4   4 TRP A   67  ALA A   80  1                                  14
HELIX    5   5 PRO A  106  ASP A  116  1                                  11
HELIX    6   6 LEU A  135  ASP A  138  5                                   4
HELIX    7   7 SER A  147  ALA A  169  1                                  23
HELIX    8   8 GLY A  180  GLU A  184  5                                   5
HELIX    9   9 ASP A  208  VAL A  222  1                                  15
HELIX   10  10 THR A  239  THR A  243  5                                   5
HELIX   11  11 GLY A  250  LEU A  253  5                                   4
HELIX   12  12 SER A  254  LEU A  284  1                                  31
HELIX   13  13 HIS A  306  GLY A  313  1                                   8
HELIX   14  14 TYR A  323  ARG A  332  1                                  10
HELIX   15  15 ARG A  345  GLN A  349  5                                   5
HELIX   16  16 SER A  350  MET A  354  5                                   5
HELIX   17  17 ALA A  356  GLU A  371  1                                  16
HELIX   18  18 ASP A  385  ARG A  397  1                                  13
HELIX   19  19 GLU A  425  HIS A  440  1                                  16
HELIX   20  20 SER A  463  GLN A  469  1                                   7
HELIX   21  21 ALA A  470  GLN A  472  5                                   3
SHEET    1  AA 9 GLN A  11  MET A  15  0
SHEET    2  AA 9 GLY A 413  TYR A 416  1  O  PHE A 414   N  TYR A  13
SHEET    3  AA 9 VAL A 375  GLU A 378  1  O  CYS A 377   N  THR A 415
SHEET    4  AA 9 SER A 336  PHE A 339  1  O  ILE A 337   N  ALA A 376
SHEET    5  AA 9 GLN A 289  LYS A 293  1  O  LEU A 290   N  SER A 336
SHEET    6  AA 9 ILE A 172  VAL A 177  1  O  VAL A 173   N  GLN A 289
SHEET    7  AA 9 LYS A  83  SER A  89  1  O  LEU A  84   N  VAL A 173
SHEET    8  AA 9 GLY A  47  TRP A  53  1  O  VAL A  48   N  GLN A  85
SHEET    9  AA 9 GLN A  11  MET A  15  1  O  VAL A  14   N  MET A  49
SHEET    1  AB 2 PHE A 120  THR A 122  0
SHEET    2  AB 2 ARG A 128  LEU A 133 -1  N  ASN A 129   O  TYR A 121
CISPEP   1 PHE A  198    PRO A  199          0        -2.34
CISPEP   2 LEU A  417    ARG A  418          0        -9.03
CISPEP   3 GLN A  472    PRO A  473          0       -10.53
SITE     1 AC1 20 ASP A  99  GLN A 192  PHE A 198  HIS A 298
SITE     2 AC1 20 ALA A 380  LEU A 381  PRO A 382  SER A 404
SITE     3 AC1 20 HOH A2400  HOH A2616  HOH A2661  HOH A2806
SITE     4 AC1 20 HOH A2807  HOH A2808  HOH A2809  HOH A2810
SITE     5 AC1 20 HOH A2811  HOH A2812  HOH A2813  HOH A2814
SITE     1 AC2  7 THR A 127  ASN A 129  PRO A 188  PRO A 191
SITE     2 AC2  7 TYR A 236  HOH A2406  HOH A2815
SITE     1 AC3  6 GLN A 212  PHE A 215  GLU A 228  PHE A 229
SITE     2 AC3  6 HOH A2816  HOH A2817
CRYST1   68.846   71.466   92.472  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      0.014525  0.000000  0.000000        0.00000
SCALE2      0.000000  0.013993  0.000000        0.00000
SCALE3      0.000000  0.000000  0.010814        0.00000
      
PROCHECK
Go to PROCHECK summary
 References