PDB Short entry for 2JFF
HEADER    LIGASE                                  01-FEB-07   2JFF              
TITLE     CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH D-GLU CONTAINING     
TITLE    2 SULFONAMIDE INHIBITOR                                                
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE;           
COMPND   3 CHAIN: A;                                                            
COMPND   4 SYNONYM: UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE LIGASE, UDP-N-    
COMPND   5 ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE SYNTHETASE, D-GLUTAMIC ACID-     
COMPND   6 ADDING ENZYME;                                                       
COMPND   7 EC: 6.3.2.9;                                                         
COMPND   8 ENGINEERED: YES;                                                     
COMPND   9 OTHER_DETAILS: INHIBITOR N-(6-BUTOXY-NAPHTHALENE-2-SULFONYL)-D-      
COMPND  10 GLUTAMIC ACID BOUND                                                  
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;                               
SOURCE   3 ORGANISM_TAXID: 562;                                                 
SOURCE   4 EXPRESSION_SYSTEM: ESCHERICHIA COLI DH5[ALPHA];                      
SOURCE   5 EXPRESSION_SYSTEM_TAXID: 668369;                                     
SOURCE   6 EXPRESSION_SYSTEM_PLASMID: PABD16                                    
KEYWDS    MURD-INHIBITOR COMPLEX, PEPTIDOGLYCAN SYNTHESIS, LIGASE, CELL WALL,   
KEYWDS   2 CELL SHAPE, CELL CYCLE, NUCLEOTIDE-BINDING, SULFONAMIDE INHIBITOR,   
KEYWDS   3 MURD LIGASE, ATP-BINDING, CELL DIVISION                              
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    M.KOTNIK,J.HUMLJAN,C.CONTRERAS-MARTEL,M.OBLAK,K.KRISTAN,M.HERVE,      
AUTHOR   2 D.BLANOT,U.URLEB,S.GOBEC,A.DESSEN,T.SOLMAJER                         
REVDAT   4   31-JAN-18 2JFF    1       SOURCE                                   
REVDAT   3   24-FEB-09 2JFF    1       VERSN                                    
REVDAT   2   12-JUN-07 2JFF    1       JRNL                                     
REVDAT   1   15-MAY-07 2JFF    0                                                
JRNL        AUTH   M.KOTNIK,J.HUMLJAN,C.CONTRERAS-MARTEL,M.OBLAK,K.KRISTAN,     
JRNL        AUTH 2 M.HERVE,D.BLANOT,U.URLEB,S.GOBEC,A.DESSEN,T.SOLMAJER         
JRNL        TITL   STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF ENANTIOMERIC   
JRNL        TITL 2 GLUTAMIC ACID DERIVATIVES AS POTENTIAL TRANSITION STATE      
JRNL        TITL 3 ANALOGUE INHIBITORS OF MURD LIGASE.                          
JRNL        REF    J.MOL.BIOL.                   V. 370   107 2007              
JRNL        REFN                   ISSN 0022-2836                               
JRNL        PMID   17507028                                                     
JRNL        DOI    10.1016/J.JMB.2007.04.048                                    
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.89 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : REFMAC 5.2.0019                                      
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) : 1.89                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 46.18                          
REMARK   3   DATA CUTOFF            (SIGMA(F)) : NULL                           
REMARK   3   COMPLETENESS FOR RANGE        (%) : 99.7                           
REMARK   3   NUMBER OF REFLECTIONS             : 42746                          
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) : 0.175                           
REMARK   3   R VALUE            (WORKING SET) : 0.173                           
REMARK   3   FREE R VALUE                     : 0.215                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.000                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 2256                            
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) : 1.89                         
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 1.94                         
REMARK   3   REFLECTION IN BIN     (WORKING SET) : 3063                         
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : NULL                         
REMARK   3   BIN R VALUE           (WORKING SET) : 0.2120                       
REMARK   3   BIN FREE R VALUE SET COUNT          : 155                          
REMARK   3   BIN FREE R VALUE                    : 0.2590                       
REMARK   3                                                                      
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
REMARK   3   PROTEIN ATOMS            : 3253                                    
REMARK   3   NUCLEIC ACID ATOMS       : 0                                       
REMARK   3   HETEROGEN ATOMS          : 38                                      
REMARK   3   SOLVENT ATOMS            : 479                                     
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : NULL                           
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 18.80                          
REMARK   3   OVERALL ANISOTROPIC B VALUE.                                       
REMARK   3    B11 (A**2) : 0.30000                                              
REMARK   3    B22 (A**2) : 0.30000                                              
REMARK   3    B33 (A**2) : -0.61000                                             
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): 0.123         
REMARK   3   ESU BASED ON FREE R VALUE                       (A): 0.123         
REMARK   3   ESU BASED ON MAXIMUM LIKELIHOOD                 (A): 0.081         
REMARK   3   ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.665         
REMARK   3                                                                      
REMARK   3 CORRELATION COEFFICIENTS.                                            
REMARK   3   CORRELATION COEFFICIENT FO-FC      : 0.952                         
REMARK   3   CORRELATION COEFFICIENT FO-FC FREE : 0.923                         
REMARK   3                                                                      
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES        COUNT    RMS    WEIGHT      
REMARK   3   BOND LENGTHS REFINED ATOMS        (A):  3366 ; 0.014 ; 0.022       
REMARK   3   BOND LENGTHS OTHERS               (A):  NULL ;  NULL ;  NULL       
REMARK   3   BOND ANGLES REFINED ATOMS   (DEGREES):  4575 ; 1.366 ; 1.982       
REMARK   3   BOND ANGLES OTHERS          (DEGREES):  NULL ;  NULL ;  NULL       
REMARK   3   TORSION ANGLES, PERIOD 1    (DEGREES):   436 ; 5.945 ; 5.000       
REMARK   3   TORSION ANGLES, PERIOD 2    (DEGREES):   143 ;32.785 ;24.685       
REMARK   3   TORSION ANGLES, PERIOD 3    (DEGREES):   552 ;12.518 ;15.000       
REMARK   3   TORSION ANGLES, PERIOD 4    (DEGREES):    20 ;15.421 ;15.000       
REMARK   3   CHIRAL-CENTER RESTRAINTS       (A**3):   530 ; 0.101 ; 0.200       
REMARK   3   GENERAL PLANES REFINED ATOMS      (A):  2528 ; 0.005 ; 0.020       
REMARK   3   GENERAL PLANES OTHERS             (A):  NULL ;  NULL ;  NULL       
REMARK   3   NON-BONDED CONTACTS REFINED ATOMS (A):  1613 ; 0.193 ; 0.200       
REMARK   3   NON-BONDED CONTACTS OTHERS        (A):  NULL ;  NULL ;  NULL       
REMARK   3   NON-BONDED TORSION REFINED ATOMS  (A):  2282 ; 0.297 ; 0.200       
REMARK   3   NON-BONDED TORSION OTHERS         (A):  NULL ;  NULL ;  NULL       
REMARK   3   H-BOND (X...Y) REFINED ATOMS      (A):   393 ; 0.158 ; 0.200       
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):    34 ; 0.183 ; 0.200       
REMARK   3   SYMMETRY VDW OTHERS               (A):  NULL ;  NULL ;  NULL       
REMARK   3   SYMMETRY H-BOND REFINED ATOMS     (A):    24 ; 0.134 ; 0.200       
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):  2221 ; 0.884 ; 1.500       
REMARK   3   MAIN-CHAIN BOND OTHER ATOMS    (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   MAIN-CHAIN ANGLE REFINED ATOMS (A**2):  3446 ; 1.362 ; 2.000       
REMARK   3   MAIN-CHAIN ANGLE OTHER ATOMS   (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   SIDE-CHAIN BOND REFINED ATOMS  (A**2):  1297 ; 2.161 ; 3.000       
REMARK   3   SIDE-CHAIN BOND OTHER ATOMS    (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   SIDE-CHAIN ANGLE REFINED ATOMS (A**2):  1126 ; 3.440 ; 4.500       
REMARK   3   SIDE-CHAIN ANGLE OTHER ATOMS   (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   LONG RANGE B REFINED ATOMS     (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   LONG RANGE B OTHER ATOMS       (A**2):  NULL ;  NULL ;  NULL       
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: THE FOLLOWING RESIDUES WERE NOT LOCATE    
REMARK   3  IN THE EXPERIMENT - GLY A 222, ALA A 223, ASP A 224, GLU A 225,     
REMARK   3  GLN A 243, GLY A 244. RESIDUES ARG A 221 AND ARG A 226 WERE         
REMARK   3  MODELED AS ALANINES DUE TO INSUFFICIENT ELECTRON DENSITY.           
REMARK   4                                                                      
REMARK   4 2JFF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-FEB-07.                  
REMARK 100 THE DEPOSITION ID IS D_1290031287.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 16-SEP-06                          
REMARK 200  TEMPERATURE           (KELVIN) : 288.0                              
REMARK 200  PH                             : 7.50                               
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : ESRF                               
REMARK 200  BEAMLINE                       : ID14-1                             
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.934                              
REMARK 200  MONOCHROMATOR                  : NULL                               
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : CCD                                
REMARK 200  DETECTOR MANUFACTURER          : ADSC CCD                           
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : XDS                                
REMARK 200  DATA SCALING SOFTWARE          : XSCALE                             
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 44144                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.890                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 50.000                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 3.000                              
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 97.9                               
REMARK 200  DATA REDUNDANCY                : 4.900                              
REMARK 200  R MERGE                    (I) : 0.06000                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 22.0000                            
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.89                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 2.00                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 93.6                               
REMARK 200  DATA REDUNDANCY IN SHELL       : 4.90                               
REMARK 200  R MERGE FOR SHELL          (I) : 0.29000                            
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 6.000                              
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT        
REMARK 200 SOFTWARE USED: PHASER                                                
REMARK 200 STARTING MODEL: PDB ENTRY 3UAG                                       
REMARK 200                                                                      
REMARK 200 REMARK: BOTH LIGANDS (UMA AND ADP), AS WELL AS THE SIDE-CHAINS OF    
REMARK 200  AMINO ACID RESIDUES WITHIN THE SUBSTRATE BINDING SITES AND ALSO     
REMARK 200  KCX198 WERE DELETED TO AVOID BIAS                                   
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 60.00                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.10                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLIZED FROM 1.7 M      
REMARK 280  (NH4)2SO4, 7% PEG 400, 100 MM HEPES, PH 7.5; THEN SOAKED IN 2 MM    
REMARK 280  OF INHIBITOR SOLUTION., PH 7.50                                     
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41                             
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,X,Z+1/4                                              
REMARK 290       4555   Y,-X,Z+3/4                                              
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       67.53000            
REMARK 290   SMTRY1   3  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY2   3  1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000       33.76500            
REMARK 290   SMTRY1   4  0.000000  1.000000  0.000000        0.00000            
REMARK 290   SMTRY2   4 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY3   4  0.000000  0.000000  1.000000      101.29500            
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: PQS                                                   
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     0                                                      
REMARK 465     GLY A   222                                                      
REMARK 465     ALA A   223                                                      
REMARK 465     ASP A   224                                                      
REMARK 465     GLU A   225                                                      
REMARK 465     GLN A   243                                                      
REMARK 465     GLY A   244                                                      
REMARK 465     HIS A   440                                                      
REMARK 465     HIS A   441                                                      
REMARK 465     HIS A   442                                                      
REMARK 465     HIS A   443                                                      
REMARK 465     HIS A   444                                                      
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 221    CG   CD   NE   CZ   NH1  NH2                        
REMARK 470     ARG A 226    CG   CD   NE   CZ   NH1  NH2                        
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  2242     O    HOH A  2243              2.11            
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    LEU A  13     -123.09    -91.31                                   
REMARK 500    PHE A 303       58.50     35.75                                   
REMARK 500    ARG A 380       79.76   -161.09                                   
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 A2021        DISTANCE =  5.83 ANGSTROMS                       
REMARK 800                                                                      
REMARK 800 SITE                                                                 
REMARK 800 SITE_IDENTIFIER: AC1                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1441                 
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC2                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1442                 
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC3                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LK2 A1440                 
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 1E0D   RELATED DB: PDB                                   
REMARK 900 UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE                    
REMARK 900 RELATED ID: 1EEH   RELATED DB: PDB                                   
REMARK 900 UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE                    
REMARK 900 RELATED ID: 1UAG   RELATED DB: PDB                                   
REMARK 900 UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE                    
REMARK 900 RELATED ID: 2UAG   RELATED DB: PDB                                   
REMARK 900 UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE                    
REMARK 900 RELATED ID: 3UAG   RELATED DB: PDB                                   
REMARK 900 UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE                    
REMARK 900 RELATED ID: 4UAG   RELATED DB: PDB                                   
REMARK 900 UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE                    
REMARK 900 RELATED ID: 2JFG   RELATED DB: PDB                                   
REMARK 900 CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH UMA AND ADP         
REMARK 900 RELATED ID: 2JFH   RELATED DB: PDB                                   
REMARK 900 CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH L-GLU CONTAINING    
REMARK 900 SULFONAMIDE INHIBITOR                                                
REMARK 999                                                                      
REMARK 999 SEQUENCE                                                             
REMARK 999 C-TERMINAL HIS-TAG (SHHHHHH)                                         
DBREF  2JFF A    0     0  PDB    2JFF     2JFF             0      0             
DBREF  2JFF A    1   437  UNP    P14900   MURD_ECOLI       1    437             
DBREF  2JFF A  438   444  PDB    2JFF     2JFF           438    444             
SEQRES   1 A  445  MET ALA ASP TYR GLN GLY LYS ASN VAL VAL ILE ILE GLY          
SEQRES   2 A  445  LEU GLY LEU THR GLY LEU SER CYS VAL ASP PHE PHE LEU          
SEQRES   3 A  445  ALA ARG GLY VAL THR PRO ARG VAL MET ASP THR ARG MET          
SEQRES   4 A  445  THR PRO PRO GLY LEU ASP LYS LEU PRO GLU ALA VAL GLU          
SEQRES   5 A  445  ARG HIS THR GLY SER LEU ASN ASP GLU TRP LEU MET ALA          
SEQRES   6 A  445  ALA ASP LEU ILE VAL ALA SER PRO GLY ILE ALA LEU ALA          
SEQRES   7 A  445  HIS PRO SER LEU SER ALA ALA ALA ASP ALA GLY ILE GLU          
SEQRES   8 A  445  ILE VAL GLY ASP ILE GLU LEU PHE CYS ARG GLU ALA GLN          
SEQRES   9 A  445  ALA PRO ILE VAL ALA ILE THR GLY SER ASN GLY LYS SER          
SEQRES  10 A  445  THR VAL THR THR LEU VAL GLY GLU MET ALA LYS ALA ALA          
SEQRES  11 A  445  GLY VAL ASN VAL GLY VAL GLY GLY ASN ILE GLY LEU PRO          
SEQRES  12 A  445  ALA LEU MET LEU LEU ASP ASP GLU CYS GLU LEU TYR VAL          
SEQRES  13 A  445  LEU GLU LEU SER SER PHE GLN LEU GLU THR THR SER SER          
SEQRES  14 A  445  LEU GLN ALA VAL ALA ALA THR ILE LEU ASN VAL THR GLU          
SEQRES  15 A  445  ASP HIS MET ASP ARG TYR PRO PHE GLY LEU GLN GLN TYR          
SEQRES  16 A  445  ARG ALA ALA KCX LEU ARG ILE TYR GLU ASN ALA LYS VAL          
SEQRES  17 A  445  CYS VAL VAL ASN ALA ASP ASP ALA LEU THR MET PRO ILE          
SEQRES  18 A  445  ARG GLY ALA ASP GLU ARG CYS VAL SER PHE GLY VAL ASN          
SEQRES  19 A  445  MET GLY ASP TYR HIS LEU ASN HIS GLN GLN GLY GLU THR          
SEQRES  20 A  445  TRP LEU ARG VAL LYS GLY GLU LYS VAL LEU ASN VAL LYS          
SEQRES  21 A  445  GLU MET LYS LEU SER GLY GLN HIS ASN TYR THR ASN ALA          
SEQRES  22 A  445  LEU ALA ALA LEU ALA LEU ALA ASP ALA ALA GLY LEU PRO          
SEQRES  23 A  445  ARG ALA SER SER LEU LYS ALA LEU THR THR PHE THR GLY          
SEQRES  24 A  445  LEU PRO HIS ARG PHE GLU VAL VAL LEU GLU HIS ASN GLY          
SEQRES  25 A  445  VAL ARG TRP ILE ASN ASP SER LYS ALA THR ASN VAL GLY          
SEQRES  26 A  445  SER THR GLU ALA ALA LEU ASN GLY LEU HIS VAL ASP GLY          
SEQRES  27 A  445  THR LEU HIS LEU LEU LEU GLY GLY ASP GLY LYS SER ALA          
SEQRES  28 A  445  ASP PHE SER PRO LEU ALA ARG TYR LEU ASN GLY ASP ASN          
SEQRES  29 A  445  VAL ARG LEU TYR CYS PHE GLY ARG ASP GLY ALA GLN LEU          
SEQRES  30 A  445  ALA ALA LEU ARG PRO GLU VAL ALA GLU GLN THR GLU THR          
SEQRES  31 A  445  MET GLU GLN ALA MET ARG LEU LEU ALA PRO ARG VAL GLN          
SEQRES  32 A  445  PRO GLY ASP MET VAL LEU LEU SER PRO ALA CYS ALA SER          
SEQRES  33 A  445  LEU ASP GLN PHE LYS ASN PHE GLU GLN ARG GLY ASN GLU          
SEQRES  34 A  445  PHE ALA ARG LEU ALA LYS GLU LEU GLY SER HIS HIS HIS          
SEQRES  35 A  445  HIS HIS HIS                                                  
MODRES 2JFF KCX A  198  LYS  LYSINE NZ-CARBOXYLIC ACID                          
HET    KCX  A 198      12                                                       
HET    LK2  A1440      28                                                       
HET    SO4  A1441       5                                                       
HET    SO4  A1442       5                                                       
HETNAM     KCX LYSINE NZ-CARBOXYLIC ACID                                        
HETNAM     LK2 N-[(6-BUTOXYNAPHTHALEN-2-YL)SULFONYL]-D-GLUTAMIC ACID            
HETNAM     SO4 SULFATE ION                                                      
FORMUL   1  KCX    C7 H14 N2 O4                                                 
FORMUL   2  LK2    C19 H23 N O7 S                                               
FORMUL   3  SO4    2(O4 S 2-)                                                   
FORMUL   5  HOH   *479(H2 O)                                                    
HELIX    1   1 LEU A   13  ALA A   26  1                                  14    
HELIX    2   2 GLY A   42  LEU A   46  5                                   5    
HELIX    3   3 ASN A   58  ALA A   65  1                                   8    
HELIX    4   4 HIS A   78  ALA A   87  1                                  10    
HELIX    5   5 GLY A   93  ALA A  102  1                                  10    
HELIX    6   6 GLY A  114  ALA A  129  1                                  16    
HELIX    7   7 PRO A  142  LEU A  147  5                                   6    
HELIX    8   8 SER A  159  THR A  165  1                                   7    
HELIX    9   9 HIS A  183  TYR A  187  5                                   5    
HELIX   10  10 PHE A  189  ARG A  200  1                                  12    
HELIX   11  11 ILE A  201  GLU A  203  5                                   3    
HELIX   12  12 ASP A  214  MET A  218  5                                   5    
HELIX   13  13 LYS A  259  MET A  261  5                                   3    
HELIX   14  14 GLY A  265  ALA A  282  1                                  18    
HELIX   15  15 PRO A  285  PHE A  296  1                                  12    
HELIX   16  16 ASN A  322  ASN A  331  1                                  10    
HELIX   17  17 PHE A  352  LEU A  359  5                                   8    
HELIX   18  18 ASP A  372  ALA A  378  1                                   7    
HELIX   19  19 LEU A  379  GLU A  382  5                                   4    
HELIX   20  20 THR A  389  ALA A  398  1                                  10    
HELIX   21  21 PRO A  399  VAL A  401  5                                   3    
HELIX   22  22 ASN A  421  GLY A  437  1                                  17    
SHEET    1  AA 5 ARG A  52  THR A  54  0                                        
SHEET    2  AA 5 ARG A  32  ASP A  35  1  O  VAL A  33   N  HIS A  53           
SHEET    3  AA 5 VAL A   8  ILE A  11  1  O  VAL A   8   N  ARG A  32           
SHEET    4  AA 5 LEU A  67  ALA A  70  1  O  LEU A  67   N  VAL A   9           
SHEET    5  AA 5 GLU A  90  VAL A  92  1  O  GLU A  90   N  ILE A  68           
SHEET    1  AB 6 VAL A 133  GLY A 137  0                                        
SHEET    2  AB 6 LEU A 153  GLU A 157  1  O  LEU A 153   N  GLY A 134           
SHEET    3  AB 6 ILE A 106  THR A 110  1  O  VAL A 107   N  LEU A 156           
SHEET    4  AB 6 ALA A 173  ILE A 176  1  O  ALA A 173   N  ALA A 108           
SHEET    5  AB 6 VAL A 207  ASN A 211  1  O  VAL A 207   N  ALA A 174           
SHEET    6  AB 6 VAL A 228  PHE A 230  1  O  VAL A 228   N  VAL A 210           
SHEET    1  AC 3 TYR A 237  HIS A 241  0                                        
SHEET    2  AC 3 THR A 246  VAL A 250 -1  O  TRP A 247   N  ASN A 240           
SHEET    3  AC 3 GLU A 253  ASN A 257 -1  O  GLU A 253   N  VAL A 250           
SHEET    1  AD 6 GLU A 304  HIS A 309  0                                        
SHEET    2  AD 6 VAL A 312  ASN A 316 -1  O  VAL A 312   N  HIS A 309           
SHEET    3  AD 6 MET A 406  LEU A 409  1  O  VAL A 407   N  ILE A 315           
SHEET    4  AD 6 LEU A 339  GLY A 344  1  O  HIS A 340   N  LEU A 408           
SHEET    5  AD 6 VAL A 364  PHE A 369  1  O  ARG A 365   N  LEU A 341           
SHEET    6  AD 6 ALA A 384  GLN A 386  1  O  GLU A 385   N  CYS A 368           
SSBOND   1 CYS A  208    CYS A  227                          1555   1555  2.03  
LINK         C   ALA A 197                 N   KCX A 198     1555   1555  1.34  
LINK         C   KCX A 198                 N   LEU A 199     1555   1555  1.34  
SITE     1 AC1  9 ASN A 113  GLY A 114  LYS A 115  SER A 116                    
SITE     2 AC1  9 THR A 117  ARG A 302  LYS A 319  HOH A2478                    
SITE     3 AC1  9 HOH A2479                                                     
SITE     1 AC2  4 HIS A 309  ASN A 310  SER A 438  HIS A 439                    
SITE     1 AC3 18 ASP A  35  ARG A  37  SER A  71  GLY A  73                    
SITE     2 AC3 18 PHE A 161  HIS A 183  LYS A 348  ALA A 414                    
SITE     3 AC3 18 SER A 415  ASN A 421  PHE A 422  HOH A2191                    
SITE     4 AC3 18 HOH A2218  HOH A2247  HOH A2474  HOH A2475                    
SITE     5 AC3 18 HOH A2476  HOH A2477                                          
CRYST1   65.288   65.288  135.060  90.00  90.00  90.00 P 41          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      0.015317  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.015317  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.007404        0.00000