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PDBsum entry 3r5f

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Ligase PDB id
3r5f
Jmol
Contents
Protein chain
343 a.a.
Ligands
ATP
Metals
_MG
Waters ×125
HEADER    LIGASE                                  18-MAR-11   3R5F
TITLE     CRYSTAL STRUCTURE OF D-ALANINE-D-ALNINE LIGASE FROM XANTHOMONAS ORYZAE
TITLE    2 PV. ORYZAE WITH ATP
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: D-ALANINE--D-ALANINE LIGASE 1;
COMPND   3 CHAIN: A;
COMPND   4 SYNONYM: D-ALA-D-ALA LIGASE 1, D-ALANYLALANINE SYNTHETASE 1;
COMPND   5 EC: 6.3.2.4;
COMPND   6 ENGINEERED: YES;
COMPND   7 MUTATION: YES
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: XANTHOMONAS ORYZAE PV. ORYZAE;
SOURCE   3 ORGANISM_TAXID: 291331;
SOURCE   4 STRAIN: KACC10331;
SOURCE   5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE   6 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE   7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE   8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE   9 EXPRESSION_SYSTEM_PLASMID: HIS-TEV-PET11A
KEYWDS    XODDL-ATP COMPLEX, ATP-GRASP DOMAIN, LIGASE
EXPDTA    X-RAY DIFFRACTION
AUTHOR    T.T.N.DOAN,J.K.KIM,L.W.KANG
REVDAT   1   25-MAY-11 3R5F    0
JRNL        AUTH   T.T.N.DOAN,J.K.KIM,L.W.KANG
JRNL        TITL   CRYSTAL STRUCTURE OF D-ALANINE-D-ALANINE LIGASE A FROM
JRNL        TITL 2 XANTHOMONAS ORYZAE PATHOVAR ORYZAE WITH ATP
JRNL        REF    TO BE PUBLISHED
JRNL        REFN
REMARK   2
REMARK   2 RESOLUTION.    2.07 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : REFMAC 5.5.0109
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) : 2.07
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 41.95
REMARK   3   DATA CUTOFF            (SIGMA(F)) : NULL
REMARK   3   COMPLETENESS FOR RANGE        (%) : 100.0
REMARK   3   NUMBER OF REFLECTIONS             : 20294
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) : 0.211
REMARK   3   R VALUE            (WORKING SET) : 0.208
REMARK   3   FREE R VALUE                     : 0.277
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.100
REMARK   3   FREE R VALUE TEST SET COUNT      : 1097
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) : 2.07
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 2.12
REMARK   3   REFLECTION IN BIN     (WORKING SET) : 1471
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 100.00
REMARK   3   BIN R VALUE           (WORKING SET) : 0.2300
REMARK   3   BIN FREE R VALUE SET COUNT          : 77
REMARK   3   BIN FREE R VALUE                    : 0.3330
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            : 2586
REMARK   3   NUCLEIC ACID ATOMS       : 0
REMARK   3   HETEROGEN ATOMS          : 32
REMARK   3   SOLVENT ATOMS            : 125
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : NULL
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 39.19
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : -0.01000
REMARK   3    B22 (A**2) : -0.01000
REMARK   3    B33 (A**2) : 0.01000
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 OVERALL COORDINATE ERROR.
REMARK   3   ESU BASED ON R VALUE                            (A): NULL
REMARK   3   ESU BASED ON FREE R VALUE                       (A): 0.216
REMARK   3   ESU BASED ON MAXIMUM LIKELIHOOD                 (A): 0.152
REMARK   3   ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.454
REMARK   3
REMARK   3 CORRELATION COEFFICIENTS.
REMARK   3   CORRELATION COEFFICIENT FO-FC      : 0.952
REMARK   3   CORRELATION COEFFICIENT FO-FC FREE : 0.915
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES        COUNT    RMS    WEIGHT
REMARK   3   BOND LENGTHS REFINED ATOMS        (A):  2676 ; 0.023 ; 0.022
REMARK   3   BOND LENGTHS OTHERS               (A):  NULL ;  NULL ;  NULL
REMARK   3   BOND ANGLES REFINED ATOMS   (DEGREES):  3643 ; 2.098 ; 1.978
REMARK   3   BOND ANGLES OTHERS          (DEGREES):  NULL ;  NULL ;  NULL
REMARK   3   TORSION ANGLES, PERIOD 1    (DEGREES):   342 ; 7.522 ; 5.000
REMARK   3   TORSION ANGLES, PERIOD 2    (DEGREES):   117 ;38.771 ;23.932
REMARK   3   TORSION ANGLES, PERIOD 3    (DEGREES):   430 ;19.745 ;15.000
REMARK   3   TORSION ANGLES, PERIOD 4    (DEGREES):    22 ;25.896 ;15.000
REMARK   3   CHIRAL-CENTER RESTRAINTS       (A**3):   429 ; 0.147 ; 0.200
REMARK   3   GENERAL PLANES REFINED ATOMS      (A):  2010 ; 0.009 ; 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):  NULL ;  NULL ;  NULL
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):  1710 ; 1.281 ; 1.500
REMARK   3   MAIN-CHAIN BOND OTHER ATOMS    (A**2):  NULL ;  NULL ;  NULL
REMARK   3   MAIN-CHAIN ANGLE REFINED ATOMS (A**2):  2733 ; 2.228 ; 2.000
REMARK   3   SIDE-CHAIN BOND REFINED ATOMS  (A**2):   966 ; 3.276 ; 3.000
REMARK   3   SIDE-CHAIN ANGLE REFINED ATOMS (A**2):   910 ; 5.277 ; 4.500
REMARK   3
REMARK   3 ANISOTROPIC THERMAL FACTOR RESTRAINTS.    COUNT   RMS   WEIGHT
REMARK   3   RIGID-BOND RESTRAINTS          (A**2):  NULL ;  NULL ;  NULL
REMARK   3   SPHERICITY; FREE ATOMS         (A**2):  NULL ;  NULL ;  NULL
REMARK   3   SPHERICITY; BONDED ATOMS       (A**2):  NULL ;  NULL ;  NULL
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
REMARK   3   PARAMETERS FOR MASK CALCULATION
REMARK   3   VDW PROBE RADIUS   : 1.40
REMARK   3   ION PROBE RADIUS   : 0.80
REMARK   3   SHRINKAGE RADIUS   : 0.80
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK   3  POSITIONS
REMARK   4
REMARK   4 3R5F COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-MAR-11.
REMARK 100 THE RCSB ID CODE IS RCSB064511.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 18-DEC-08
REMARK 200  TEMPERATURE           (KELVIN) : 100
REMARK 200  PH                             : 8.5
REMARK 200  NUMBER OF CRYSTALS USED        : 1
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : Y
REMARK 200  RADIATION SOURCE               : PAL/PLS
REMARK 200  BEAMLINE                       : 4A
REMARK 200  X-RAY GENERATOR MODEL          : NULL
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.00000
REMARK 200  MONOCHROMATOR                  : NULL
REMARK 200  OPTICS                         : NULL
REMARK 200
REMARK 200  DETECTOR TYPE                  : CCD
REMARK 200  DETECTOR MANUFACTURER          : ADSC QUANTUM 270
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : NULL
REMARK 200  DATA SCALING SOFTWARE          : NULL
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 21461
REMARK 200  RESOLUTION RANGE HIGH      (A) : 2.070
REMARK 200  RESOLUTION RANGE LOW       (A) : 50.000
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 99.8
REMARK 200  DATA REDUNDANCY                : NULL
REMARK 200  R MERGE                    (I) : NULL
REMARK 200  R SYM                      (I) : NULL
REMARK 200   FOR THE DATA SET  : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : NULL
REMARK 200  COMPLETENESS FOR SHELL     (%) : NULL
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL
REMARK 200  R MERGE FOR SHELL          (I) : NULL
REMARK 200  R SYM FOR SHELL            (I) : NULL
REMARK 200   FOR SHELL         : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: NULL
REMARK 200 STARTING MODEL: PDB ENTRY 3E5N
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 38.93
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.001ML OF 6 MG/ML PROTEIN WAS MIXED
REMARK 280  TO 0.001ML OF A MOTHER LIQUOR, CONTAINING 30%(W/V) PEG 4000, 0.1M
REMARK 280  TRIS PH 8.0, 0.2M MGCL2, VAPOR DIFFUSION, SITTING DROP,
REMARK 280  TEMPERATURE 283K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2
REMARK 290
REMARK 290      SYMOP   SYMMETRY
REMARK 290     NNNMMM   OPERATOR
REMARK 290       1555   X,Y,Z
REMARK 290       2555   -X,-Y,Z+1/2
REMARK 290       3555   -Y+1/2,X+1/2,Z+3/4
REMARK 290       4555   Y+1/2,-X+1/2,Z+1/4
REMARK 290       5555   -X+1/2,Y+1/2,-Z+3/4
REMARK 290       6555   X+1/2,-Y+1/2,-Z+1/4
REMARK 290       7555   Y,X,-Z
REMARK 290       8555   -Y,-X,-Z+1/2
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        0.00000
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       48.57150
REMARK 290   SMTRY1   3  0.000000 -1.000000  0.000000       41.61250
REMARK 290   SMTRY2   3  1.000000  0.000000  0.000000       41.61250
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000       72.85725
REMARK 290   SMTRY1   4  0.000000  1.000000  0.000000       41.61250
REMARK 290   SMTRY2   4 -1.000000  0.000000  0.000000       41.61250
REMARK 290   SMTRY3   4  0.000000  0.000000  1.000000       24.28575
REMARK 290   SMTRY1   5 -1.000000  0.000000  0.000000       41.61250
REMARK 290   SMTRY2   5  0.000000  1.000000  0.000000       41.61250
REMARK 290   SMTRY3   5  0.000000  0.000000 -1.000000       72.85725
REMARK 290   SMTRY1   6  1.000000  0.000000  0.000000       41.61250
REMARK 290   SMTRY2   6  0.000000 -1.000000  0.000000       41.61250
REMARK 290   SMTRY3   6  0.000000  0.000000 -1.000000       24.28575
REMARK 290   SMTRY1   7  0.000000  1.000000  0.000000        0.00000
REMARK 290   SMTRY2   7  1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY3   7  0.000000  0.000000 -1.000000        0.00000
REMARK 290   SMTRY1   8  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY2   8 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY3   8  0.000000  0.000000 -1.000000       48.57150
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: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 4490 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 27170 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 KCAL/MOL
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 350   BIOMT1   2  0.000000 -1.000000  0.000000        0.00000
REMARK 350   BIOMT2   2 -1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT3   2  0.000000  0.000000 -1.000000       48.57150
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     HIS A   -16
REMARK 465     HIS A   -15
REMARK 465     HIS A   -14
REMARK 465     HIS A   -13
REMARK 465     HIS A   -12
REMARK 465     HIS A   -11
REMARK 465     HIS A   -10
REMARK 465     SER A    -9
REMARK 465     SER A    -8
REMARK 465     GLU A    -7
REMARK 465     ASN A    -6
REMARK 465     LEU A    -5
REMARK 465     TYR A    -4
REMARK 465     PHE A    -3
REMARK 465     GLN A    -2
REMARK 465     GLY A    -1
REMARK 465     HIS A     0
REMARK 465     MET A     1
REMARK 465     ARG A     2
REMARK 465     PRO A    92
REMARK 465     GLU A    93
REMARK 465     GLN A    94
REMARK 465     HIS A   250
REMARK 465     ASP A   251
REMARK 465     ALA A   252
REMARK 465     PHE A   253
REMARK 465     TYR A   254
REMARK 465     SER A   255
REMARK 465     TYR A   256
REMARK 465     ALA A   257
REMARK 465     THR A   258
REMARK 465     LYS A   259
REMARK 465     TYR A   260
REMARK 465     ILE A   261
REMARK 465     SER A   262
REMARK 465     GLU A   263
REMARK 465     HIS A   264
REMARK 465     GLY A   265
REMARK 465     ALA A   266
REMARK 465     LEU A   366
REMARK 465     HIS A   367
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    ALA A 307   N   -  CA  -  C   ANGL. DEV. = -16.3 DEGREES
REMARK 500    ASP A 308   N   -  CA  -  C   ANGL. DEV. =  18.6 DEGREES
REMARK 500    GLY A 309   C   -  N   -  CA  ANGL. DEV. =  14.9 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    ASN A 236      -97.34    -98.43
REMARK 500    ASP A 308       10.90     96.03
REMARK 500    VAL A 364      156.42    138.32
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS
REMARK 500
REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH
REMARK 500 CIS AND TRANS CONFORMATION.  CIS BONDS, IF ANY, ARE LISTED
REMARK 500 ON CISPEP RECORDS.  TRANS IS DEFINED AS 180 +/- 30 AND
REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES.
REMARK 500                                 MODEL     OMEGA
REMARK 500 ASP A  308     GLY A  309                  -74.75
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CHIRAL CENTERS
REMARK 500
REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL
REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY
REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR
REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE
REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16)
REMARK 500
REMARK 500  M RES CSSEQI    IMPROPER   EXPECTED   FOUND DETAILS
REMARK 500    ASP A 308        18.3      L          L   OUTSIDE RANGE
REMARK 500
REMARK 500 REMARK: NULL
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                              MG A 369  MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH A 480   O
REMARK 620 2 ASP A 302   OD2  61.3
REMARK 620 3 ATP A 368   O1A 113.7 174.9
REMARK 620 4 ATP A 368   O3G  72.4 120.3  56.2
REMARK 620 N                    1     2     3
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP A 368
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 369
DBREF  3R5F A    1   367  UNP    Q2P8P8   Q2P8P8_XANOM     1    367
SEQADV 3R5F HIS A  -16  UNP  Q2P8P8              EXPRESSION TAG
SEQADV 3R5F HIS A  -15  UNP  Q2P8P8              EXPRESSION TAG
SEQADV 3R5F HIS A  -14  UNP  Q2P8P8              EXPRESSION TAG
SEQADV 3R5F HIS A  -13  UNP  Q2P8P8              EXPRESSION TAG
SEQADV 3R5F HIS A  -12  UNP  Q2P8P8              EXPRESSION TAG
SEQADV 3R5F HIS A  -11  UNP  Q2P8P8              EXPRESSION TAG
SEQADV 3R5F HIS A  -10  UNP  Q2P8P8              EXPRESSION TAG
SEQADV 3R5F SER A   -9  UNP  Q2P8P8              EXPRESSION TAG
SEQADV 3R5F SER A   -8  UNP  Q2P8P8              EXPRESSION TAG
SEQADV 3R5F GLU A   -7  UNP  Q2P8P8              EXPRESSION TAG
SEQADV 3R5F ASN A   -6  UNP  Q2P8P8              EXPRESSION TAG
SEQADV 3R5F LEU A   -5  UNP  Q2P8P8              EXPRESSION TAG
SEQADV 3R5F TYR A   -4  UNP  Q2P8P8              EXPRESSION TAG
SEQADV 3R5F PHE A   -3  UNP  Q2P8P8              EXPRESSION TAG
SEQADV 3R5F GLN A   -2  UNP  Q2P8P8              EXPRESSION TAG
SEQADV 3R5F GLY A   -1  UNP  Q2P8P8              EXPRESSION TAG
SEQADV 3R5F HIS A    0  UNP  Q2P8P8              EXPRESSION TAG
SEQADV 3R5F VAL A  327  UNP  Q2P8P8    MET   327 ENGINEERED MUTATION
SEQRES   1 A  384  HIS HIS HIS HIS HIS HIS HIS SER SER GLU ASN LEU TYR
SEQRES   2 A  384  PHE GLN GLY HIS MET ARG LYS ILE ARG VAL GLY LEU ILE
SEQRES   3 A  384  PHE GLY GLY LYS SER ALA GLU HIS GLU VAL SER LEU GLN
SEQRES   4 A  384  SER ALA ARG ASN ILE LEU ASP ALA LEU ASP PRO GLN ARG
SEQRES   5 A  384  PHE GLU PRO VAL LEU ILE GLY ILE ASP LYS GLN GLY GLN
SEQRES   6 A  384  TRP HIS VAL ASN ASP PRO ASP SER PHE LEU LEU HIS ALA
SEQRES   7 A  384  ASP ASP PRO ALA ARG ILE ALA LEU HIS ARG SER GLY ARG
SEQRES   8 A  384  GLY VAL ALA LEU LEU PRO GLY ALA GLN GLN GLN GLN LEU
SEQRES   9 A  384  ARG PRO ILE GLN PRO GLU GLN ALA LEU ALA GLN ILE ASP
SEQRES  10 A  384  VAL VAL PHE PRO ILE VAL HIS GLY THR LEU GLY GLU ASP
SEQRES  11 A  384  GLY SER LEU GLN GLY LEU LEU ARG MET ALA ASN LEU PRO
SEQRES  12 A  384  PHE VAL GLY SER GLY VAL LEU GLY SER ALA VAL ALA MET
SEQRES  13 A  384  ASP LYS ASP MET ALA LYS ARG VAL LEU ARG ASP ALA ARG
SEQRES  14 A  384  LEU ALA VAL ALA PRO PHE VAL CYS PHE ASP ARG HIS THR
SEQRES  15 A  384  ALA ALA HIS ALA ASP VAL ASP THR LEU ILE ALA GLN LEU
SEQRES  16 A  384  GLY LEU PRO LEU PHE VAL LYS PRO ALA ASN GLN GLY SER
SEQRES  17 A  384  SER VAL GLY VAL SER GLN VAL ARG THR ALA ASP ALA PHE
SEQRES  18 A  384  ALA ALA ALA LEU ALA LEU ALA LEU ALA TYR ASP HIS LYS
SEQRES  19 A  384  VAL LEU VAL GLU ALA ALA VAL ALA GLY ARG GLU ILE GLU
SEQRES  20 A  384  CYS ALA VAL LEU GLY ASN ALA VAL PRO HIS ALA SER VAL
SEQRES  21 A  384  CYS GLY GLU VAL VAL VAL HIS ASP ALA PHE TYR SER TYR
SEQRES  22 A  384  ALA THR LYS TYR ILE SER GLU HIS GLY ALA GLU ILE VAL
SEQRES  23 A  384  ILE PRO ALA ASP ILE ASP ALA GLN THR GLN GLN ARG ILE
SEQRES  24 A  384  GLN GLN ILE ALA VAL GLN ALA TYR GLN ALA LEU GLY CYS
SEQRES  25 A  384  ALA GLY MET ALA ARG VAL ASP VAL PHE LEU CYS ALA ASP
SEQRES  26 A  384  GLY ARG ILE VAL ILE ASN GLU VAL ASN THR LEU PRO GLY
SEQRES  27 A  384  PHE THR ARG ILE SER VAL TYR PRO LYS LEU TRP GLN ALA
SEQRES  28 A  384  SER GLY LEU ASP TYR ARG GLY LEU ILE THR ARG LEU ILE
SEQRES  29 A  384  GLU LEU ALA LEU GLU ARG HIS THR ASP ASP GLN LEU LEU
SEQRES  30 A  384  ARG SER ALA VAL GLU LEU HIS
HET    ATP  A 368      31
HET     MG  A 369       1
HETNAM     ATP ADENOSINE-5'-TRIPHOSPHATE
HETNAM      MG MAGNESIUM ION
FORMUL   2  ATP    C10 H16 N5 O13 P3
FORMUL   3   MG    MG 2+
FORMUL   4  HOH   *125(H2 O)
HELIX    1   1 GLU A   16  LEU A   31  1                                  16
HELIX    2   2 GLY A  108  ASP A  113  1                                   6
HELIX    3   3 GLY A  114  ALA A  123  1                                  10
HELIX    4   4 GLY A  131  ASP A  140  1                                  10
HELIX    5   5 ASP A  140  ALA A  151  1                                  12
HELIX    6   6 ARG A  163  ALA A  167  1                                   5
HELIX    7   7 ASP A  170  GLY A  179  1                                  10
HELIX    8   8 THR A  200  ASP A  202  5                                   3
HELIX    9   9 ALA A  203  LEU A  212  1                                  10
HELIX   10  10 ASP A  275  GLY A  294  1                                  20
HELIX   11  11 SER A  326  ALA A  334  1                                   9
HELIX   12  12 ASP A  338  ALA A  363  1                                  26
SHEET    1   A 4 TRP A  49  ASN A  52  0
SHEET    2   A 4 PHE A  36  ILE A  43 -1  N  GLY A  42   O  HIS A  50
SHEET    3   A 4 ILE A   4  GLY A  11  1  N  VAL A   6   O  GLU A  37
SHEET    4   A 4 VAL A 101  VAL A 106  1  O  VAL A 101   N  GLY A   7
SHEET    1   B 2 LEU A  58  LEU A  59  0
SHEET    2   B 2 ALA A  68  LEU A  69 -1  O  ALA A  68   N  LEU A  59
SHEET    1   C 2 VAL A  76  LEU A  78  0
SHEET    2   C 2 LEU A  87  PRO A  89 -1  O  ARG A  88   N  ALA A  77
SHEET    1   D 6 ALA A 154  VAL A 155  0
SHEET    2   D 6 ILE A 311  ASN A 317  1  O  ILE A 313   N  ALA A 154
SHEET    3   D 6 MET A 298  LEU A 305 -1  N  ARG A 300   O  ASN A 317
SHEET    4   D 6 ARG A 227  LEU A 234 -1  N  CYS A 231   O  VAL A 301
SHEET    5   D 6 HIS A 240  VAL A 247 -1  O  HIS A 240   N  LEU A 234
SHEET    6   D 6 ILE A 268  VAL A 269 -1  O  VAL A 269   N  GLU A 246
SHEET    1   E 4 PHE A 158  ASP A 162  0
SHEET    2   E 4 LYS A 217  ALA A 222 -1  O  VAL A 218   N  PHE A 161
SHEET    3   E 4 LEU A 182  PRO A 186 -1  N  LYS A 185   O  LEU A 219
SHEET    4   E 4 SER A 196  VAL A 198 -1  O  VAL A 198   N  LEU A 182
LINK        MG    MG A 369                 O   HOH A 480     1555   1555  2.62
LINK         OD2 ASP A 302                MG    MG A 369     1555   1555  2.63
LINK         O1A ATP A 368                MG    MG A 369     1555   1555  2.77
LINK         O3G ATP A 368                MG    MG A 369     1555   1555  2.88
CISPEP   1 LEU A  180    PRO A  181          0        -2.42
CISPEP   2 ILE A  270    PRO A  271          0        -8.31
SITE     1 AC1 16 LYS A 141  PHE A 183  LYS A 185  SER A 191
SITE     2 AC1 16 SER A 192  GLU A 221  ALA A 222  ALA A 223
SITE     3 AC1 16 VAL A 224  GLU A 228  PHE A 304  ASN A 314
SITE     4 AC1 16 GLU A 315   MG A 369  HOH A 476  HOH A 479
SITE     1 AC2  5 ASP A 302  ASN A 314  GLU A 315  ATP A 368
SITE     2 AC2  5 HOH A 480
CRYST1   83.225   83.225   97.143  90.00  90.00  90.00 P 43 21 2     8
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      0.012016  0.000000  0.000000        0.00000
SCALE2      0.000000  0.012016  0.000000        0.00000
SCALE3      0.000000  0.000000  0.010294        0.00000
      
PROCHECK
Go to PROCHECK summary
 References