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Database: PDB
Entry: 3RFC
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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  <I/SIGMA(I)> 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  <I/SIGMA(I)> 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                         
(ATOM LINES ARE NOT SHOWN.)
END                                                                             
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