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PDBsum entry 3rfc

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Ligase PDB id
3rfc
Jmol
Contents
Protein chain
344 a.a.
Ligands
ADP
Metals
_MG
Waters ×138
HEADER    LIGASE                                  06-APR-11   3RFC
TITLE     CRYSTAL STRUCTURE OF D-ALANINE-D-ALANINE LIGASE A FROM XANTHOMONAS
TITLE    2 ORYZAE PATHOVAR ORYZAE WITH ADP
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: D-ALANINE--D-ALANINE LIGASE 1;
COMPND   3 CHAIN: A;
COMPND   4 SYNONYM: D-ALANINE-D-ALANINE LIGASE A, D-ALA-D-ALA LIGASE 1, D-
COMPND   5 ALANYLALANINE SYNTHETASE 1;
COMPND   6 EC: 6.3.2.4;
COMPND   7 ENGINEERED: YES;
COMPND   8 MUTATION: YES
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: XANTHOMONAS ORYZAE PV. ORYZAE;
SOURCE   3 ORGANISM_TAXID: 342109;
SOURCE   4 STRAIN: MAFF 311018;
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: MODIFIED PET11A
KEYWDS    ADP FORMING LIGASE, DIMERIZATION OF TWO D-ALANINES, LIGASE
EXPDTA    X-RAY DIFFRACTION
AUTHOR    T.T.N.DOAN,J.K.KIM,Y.J.AHN,L.W.KANG
REVDAT   1   04-MAY-11 3RFC    0
JRNL        AUTH   T.T.N.DOAN,J.K.KIM,Y.J.AHN,L.W.KANG
JRNL        TITL   CRYSTAL STRUCTURE OF D-ALANINE-D-ALANINE LIGASE A FROM
JRNL        TITL 2 XANTHOMONAS ORYZAE PATHOVAR ORYZAE WITH ADP
JRNL        REF    TO BE PUBLISHED
JRNL        REFN
REMARK   2
REMARK   2 RESOLUTION.    2.10 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) : 2.10
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 38.32
REMARK   3   DATA CUTOFF            (SIGMA(F)) : NULL
REMARK   3   COMPLETENESS FOR RANGE        (%) : 99.7
REMARK   3   NUMBER OF REFLECTIONS             : 19620
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) : 0.208
REMARK   3   R VALUE            (WORKING SET) : 0.204
REMARK   3   FREE R VALUE                     : 0.282
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.100
REMARK   3   FREE R VALUE TEST SET COUNT      : 1063
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) : 2.10
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 2.15
REMARK   3   REFLECTION IN BIN     (WORKING SET) : 1375
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 99.12
REMARK   3   BIN R VALUE           (WORKING SET) : 0.2430
REMARK   3   BIN FREE R VALUE SET COUNT          : 86
REMARK   3   BIN FREE R VALUE                    : 0.3090
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            : 2597
REMARK   3   NUCLEIC ACID ATOMS       : 0
REMARK   3   HETEROGEN ATOMS          : 28
REMARK   3   SOLVENT ATOMS            : 138
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : NULL
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 35.92
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): 0.227
REMARK   3   ESU BASED ON MAXIMUM LIKELIHOOD                 (A): 0.160
REMARK   3   ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.899
REMARK   3
REMARK   3 CORRELATION COEFFICIENTS.
REMARK   3   CORRELATION COEFFICIENT FO-FC      : 0.947
REMARK   3   CORRELATION COEFFICIENT FO-FC FREE : 0.895
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES        COUNT    RMS    WEIGHT
REMARK   3   BOND LENGTHS REFINED ATOMS        (A):  2655 ; 0.021 ; 0.022
REMARK   3   BOND LENGTHS OTHERS               (A):  NULL ;  NULL ;  NULL
REMARK   3   BOND ANGLES REFINED ATOMS   (DEGREES):  3611 ; 1.989 ; 1.975
REMARK   3   BOND ANGLES OTHERS          (DEGREES):  NULL ;  NULL ;  NULL
REMARK   3   TORSION ANGLES, PERIOD 1    (DEGREES):   339 ; 7.776 ; 5.000
REMARK   3   TORSION ANGLES, PERIOD 2    (DEGREES):   116 ;38.843 ;23.879
REMARK   3   TORSION ANGLES, PERIOD 3    (DEGREES):   427 ;18.615 ;15.000
REMARK   3   TORSION ANGLES, PERIOD 4    (DEGREES):    22 ;22.605 ;15.000
REMARK   3   CHIRAL-CENTER RESTRAINTS       (A**3):   426 ; 0.144 ; 0.200
REMARK   3   GENERAL PLANES REFINED ATOMS      (A):  1994 ; 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):  1699 ; 1.154 ; 1.500
REMARK   3   MAIN-CHAIN BOND OTHER ATOMS    (A**2):  NULL ;  NULL ;  NULL
REMARK   3   MAIN-CHAIN ANGLE REFINED ATOMS (A**2):  2715 ; 2.059 ; 2.000
REMARK   3   SIDE-CHAIN BOND REFINED ATOMS  (A**2):   956 ; 3.137 ; 3.000
REMARK   3   SIDE-CHAIN ANGLE REFINED ATOMS (A**2):   896 ; 5.112 ; 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 3RFC COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-APR-11.
REMARK 100 THE RCSB ID CODE IS RCSB064860.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 11-JUN-10
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) : 0.96418
REMARK 200  MONOCHROMATOR                  : GRAPHITE
REMARK 200  OPTICS                         : NULL
REMARK 200
REMARK 200  DETECTOR TYPE                  : CCD
REMARK 200  DETECTOR MANUFACTURER          : ADSC QUANTUM 210
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200  DATA SCALING SOFTWARE          : SCALEPACK
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 20817
REMARK 200  RESOLUTION RANGE HIGH      (A) : 2.100
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     (%) : NULL
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: MOLREP
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 39.65
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 400, 0.1M TRIS 8.5, 0.2M
REMARK 280  MAGNESIUM CHLORIDE, 0.3 M DIMETHYLETHYL-(3-SULFOPROPYL)-AMMONIUM,
REMARK 280  VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 285K
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       49.13850
REMARK 290   SMTRY1   3  0.000000 -1.000000  0.000000       41.61800
REMARK 290   SMTRY2   3  1.000000  0.000000  0.000000       41.61800
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000       73.70775
REMARK 290   SMTRY1   4  0.000000  1.000000  0.000000       41.61800
REMARK 290   SMTRY2   4 -1.000000  0.000000  0.000000       41.61800
REMARK 290   SMTRY3   4  0.000000  0.000000  1.000000       24.56925
REMARK 290   SMTRY1   5 -1.000000  0.000000  0.000000       41.61800
REMARK 290   SMTRY2   5  0.000000  1.000000  0.000000       41.61800
REMARK 290   SMTRY3   5  0.000000  0.000000 -1.000000       73.70775
REMARK 290   SMTRY1   6  1.000000  0.000000  0.000000       41.61800
REMARK 290   SMTRY2   6  0.000000 -1.000000  0.000000       41.61800
REMARK 290   SMTRY3   6  0.000000  0.000000 -1.000000       24.56925
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       49.13850
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: 4070 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 28280 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.0 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       49.13850
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     PRO A    92
REMARK 465     GLU A    93
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     GLU A   365
REMARK 465     LEU A   366
REMARK 465     HIS A   367
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      -91.79   -107.29
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 A 420        DISTANCE =  5.28 ANGSTROMS
REMARK 525    HOH A 483        DISTANCE =  5.45 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                              MG A 369  MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ADP A 368   O1A
REMARK 620 2 HOH A 447   O   112.6
REMARK 620 3 ASP A 302   OD2 169.6  57.3
REMARK 620 N                    1     2
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP 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
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3E5N   RELATED DB: PDB
REMARK 900 CRYSTAL STRUCUTRE OF D-ALANINE-D-ALANINE LIGASE FROM
REMARK 900 XANTHOMONAS ORYZAE PV. ORYZAE KACC10331
DBREF  3RFC A    1   367  UNP    Q2P8P8   Q2P8P8_XANOM     1    367
SEQADV 3RFC HIS A  -16  UNP  Q2P8P8              EXPRESSION TAG
SEQADV 3RFC HIS A  -15  UNP  Q2P8P8              EXPRESSION TAG
SEQADV 3RFC HIS A  -14  UNP  Q2P8P8              EXPRESSION TAG
SEQADV 3RFC HIS A  -13  UNP  Q2P8P8              EXPRESSION TAG
SEQADV 3RFC HIS A  -12  UNP  Q2P8P8              EXPRESSION TAG
SEQADV 3RFC HIS A  -11  UNP  Q2P8P8              EXPRESSION TAG
SEQADV 3RFC HIS A  -10  UNP  Q2P8P8              EXPRESSION TAG
SEQADV 3RFC SER A   -9  UNP  Q2P8P8              EXPRESSION TAG
SEQADV 3RFC SER A   -8  UNP  Q2P8P8              EXPRESSION TAG
SEQADV 3RFC GLU A   -7  UNP  Q2P8P8              EXPRESSION TAG
SEQADV 3RFC ASN A   -6  UNP  Q2P8P8              EXPRESSION TAG
SEQADV 3RFC LEU A   -5  UNP  Q2P8P8              EXPRESSION TAG
SEQADV 3RFC TYR A   -4  UNP  Q2P8P8              EXPRESSION TAG
SEQADV 3RFC PHE A   -3  UNP  Q2P8P8              EXPRESSION TAG
SEQADV 3RFC GLN A   -2  UNP  Q2P8P8              EXPRESSION TAG
SEQADV 3RFC GLY A   -1  UNP  Q2P8P8              EXPRESSION TAG
SEQADV 3RFC HIS A    0  UNP  Q2P8P8              EXPRESSION TAG
SEQADV 3RFC 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    ADP  A 368      27
HET     MG  A 369       1
HETNAM     ADP ADENOSINE-5'-DIPHOSPHATE
HETNAM      MG MAGNESIUM ION
FORMUL   2  ADP    C10 H15 N5 O10 P2
FORMUL   3   MG    MG 2+
FORMUL   4  HOH   *138(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  ASP A  215  1                                  13
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  ARG A  361  1                                  24
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  VAL A  39
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 4 PHE A 158  ASP A 162  0
SHEET    2   D 4 LYS A 217  ALA A 222 -1  O  VAL A 218   N  PHE A 161
SHEET    3   D 4 LEU A 182  PRO A 186 -1  N  LYS A 185   O  LEU A 219
SHEET    4   D 4 SER A 196  VAL A 198 -1  O  VAL A 198   N  LEU A 182
SHEET    1   E 5 ILE A 268  VAL A 269  0
SHEET    2   E 5 HIS A 240  VAL A 247 -1  N  GLU A 246   O  VAL A 269
SHEET    3   E 5 ARG A 227  GLY A 235 -1  N  GLU A 228   O  VAL A 247
SHEET    4   E 5 GLY A 297  LEU A 305 -1  O  VAL A 301   N  CYS A 231
SHEET    5   E 5 ILE A 311  ASN A 317 -1  O  VAL A 312   N  PHE A 304
LINK         O1A ADP A 368                MG    MG A 369     1555   1555  2.57
LINK        MG    MG A 369                 O   HOH A 447     1555   1555  2.64
LINK         OD2 ASP A 302                MG    MG A 369     1555   1555  2.76
CISPEP   1 LEU A  180    PRO A  181          0        -7.31
CISPEP   2 GLY A  190    SER A  191          0       -18.93
CISPEP   3 ILE A  270    PRO A  271          0        -5.82
CISPEP   4 ASP A  308    GLY A  309          0       -12.46
SITE     1 AC1 15 PHE A 183  LYS A 185  SER A 192  GLU A 221
SITE     2 AC1 15 ALA A 222  ALA A 223  VAL A 224  GLU A 228
SITE     3 AC1 15 PHE A 304  ASN A 314  GLU A 315   MG A 369
SITE     4 AC1 15 HOH A 486  HOH A 489  HOH A 507
SITE     1 AC2  5 ASP A 302  ASN A 314  GLU A 315  ADP A 368
SITE     2 AC2  5 HOH A 447
CRYST1   83.236   83.236   98.277  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      0.012014  0.000000  0.000000        0.00000
SCALE2      0.000000  0.012014  0.000000        0.00000
SCALE3      0.000000  0.000000  0.010175        0.00000
      
PROCHECK
Go to PROCHECK summary
 References