HEADER LIGASE 10-FEB-10 2X5O TITLE DISCOVERY OF NOVEL 5-BENZYLIDENERHODANINE- AND 5-BENZYLIDENE- TITLE 2 THIAZOLIDINE-2,4-DIONE INHIBITORS OF MURD LIGASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 2-438; COMPND 5 SYNONYM: UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE SYNTHETASE, D- COMPND 6 GLUTAMIC ACID-ADDING ENZYMEMURD LIGASE; COMPND 7 EC: 6.3.2.9; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI DH5[ALPHA]; SOURCE 3 ORGANISM_TAXID: 668369; SOURCE 4 STRAIN: DH5[ALPHA]; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI DH5[ALPHA]; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 668369; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PABD16/MURD KEYWDS ATP-BINDING, CELL CYCLE, CELL DIVISION, CELL SHAPE, CELL WALL KEYWDS 2 BIOGENESIS/DEGRADATION, LIGASE, PEPTIDOGLYCAN SYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR N.ZIDAR,T.TOMASIC,R.SINK,V.RUPNIK,A.KOVAC,S.TURK,C.CONTRERAS-MARTEL, AUTHOR 2 A.DESSEN,D.BLANOT,S.GOBEC,A.ZEGA,L.PETERLIN-MASIC,D.KIKELJA REVDAT 3 28-FEB-18 2X5O 1 SOURCE JRNL REVDAT 2 31-AUG-11 2X5O 1 JRNL REMARK VERSN REVDAT 1 15-SEP-10 2X5O 0 JRNL AUTH N.ZIDAR,T.TOMASIC,R.SINK,V.RUPNIK,A.KOVAC,S.TURK,D.PATIN, JRNL AUTH 2 D.BLANOT,C.CONTRERAS MARTEL,A.DESSEN,M.MULLER PREMRU,A.ZEGA, JRNL AUTH 3 S.GOBEC,L.PETERLIN MASIC,D.KIKELJ JRNL TITL DISCOVERY OF NOVEL 5-BENZYLIDENERHODANINE AND JRNL TITL 2 5-BENZYLIDENETHIAZOLIDINE-2,4-DIONE INHIBITORS OF MURD JRNL TITL 3 LIGASE. JRNL REF J. MED. CHEM. V. 53 6584 2010 JRNL REFN ISSN 1520-4804 JRNL PMID 20804196 JRNL DOI 10.1021/JM100285G REMARK 2 REMARK 2 RESOLUTION. 1.46 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) : 1.46 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.36 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 89100 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) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4707 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) : 1.46 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.50 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4249 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3410 REMARK 3 BIN FREE R VALUE SET COUNT : 226 REMARK 3 BIN FREE R VALUE : 0.3350 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3304 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 55 REMARK 3 SOLVENT ATOMS : 535 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.23 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.81 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : NULL REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; NULL ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL 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): 2243 ; 1.532 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3603 ; 2.286 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1306 ; 3.489 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1219 ; 5.038 ; 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 : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 92 REMARK 3 ORIGIN FOR THE GROUP (A): -27.5371 36.1459 15.0677 REMARK 3 T TENSOR REMARK 3 T11: 0.0105 T22: 0.0226 REMARK 3 T33: 0.0064 T12: 0.0068 REMARK 3 T13: -0.0002 T23: -0.0102 REMARK 3 L TENSOR REMARK 3 L11: 2.4003 L22: 2.8893 REMARK 3 L33: 3.0359 L12: -0.3562 REMARK 3 L13: -0.4851 L23: 0.4325 REMARK 3 S TENSOR REMARK 3 S11: 0.0129 S12: -0.0794 S13: 0.0541 REMARK 3 S21: -0.0047 S22: 0.0021 S23: 0.0100 REMARK 3 S31: -0.1685 S32: -0.0558 S33: -0.0151 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 94 A 295 REMARK 3 ORIGIN FOR THE GROUP (A): -5.5223 19.3856 4.4038 REMARK 3 T TENSOR REMARK 3 T11: 0.0215 T22: 0.0288 REMARK 3 T33: 0.0160 T12: -0.0020 REMARK 3 T13: 0.0089 T23: 0.0018 REMARK 3 L TENSOR REMARK 3 L11: 1.8296 L22: 0.7108 REMARK 3 L33: 1.4825 L12: -0.3404 REMARK 3 L13: -0.5840 L23: 0.0561 REMARK 3 S TENSOR REMARK 3 S11: -0.0033 S12: 0.0430 S13: -0.0968 REMARK 3 S21: -0.0720 S22: -0.0381 S23: -0.0628 REMARK 3 S31: 0.0593 S32: 0.1290 S33: 0.0414 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 304 A 439 REMARK 3 ORIGIN FOR THE GROUP (A): 8.5520 29.2376 27.1570 REMARK 3 T TENSOR REMARK 3 T11: 0.0075 T22: 0.0403 REMARK 3 T33: 0.0273 T12: -0.0065 REMARK 3 T13: 0.0068 T23: -0.0096 REMARK 3 L TENSOR REMARK 3 L11: 3.4454 L22: 2.1613 REMARK 3 L33: 1.6599 L12: 1.0181 REMARK 3 L13: 0.1994 L23: 0.0525 REMARK 3 S TENSOR REMARK 3 S11: 0.0445 S12: -0.1363 S13: -0.0121 REMARK 3 S21: 0.0978 S22: 0.0116 S23: -0.0217 REMARK 3 S31: -0.0096 S32: 0.0968 S33: -0.0561 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B REMARK 3 FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U REMARK 3 FACTORS. REMARK 4 REMARK 4 2X5O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-FEB-10. REMARK 100 THE DEPOSITION ID IS D_1290042857. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAY-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM30A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9797 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 : 93804 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.460 REMARK 200 RESOLUTION RANGE LOW (A) : 47.360 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.2 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.46 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 52.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.41000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 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: NONE 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: 1.8 M (NH4)2SO4, 7% PEG 400, 100 MM REMARK 280 NACL, 100MM HEPES, PH 7.5 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 67.89050 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 33.94525 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 101.83575 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 -122.31 -96.43 REMARK 500 PRO A 142 141.39 -35.25 REMARK 500 ALA A 223 -104.25 -110.73 REMARK 500 GLU A 225 39.76 -151.79 REMARK 500 VAL A 232 -63.33 -90.06 REMARK 500 GLN A 243 -121.73 45.50 REMARK 500 ARG A 380 83.69 -158.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ARG A 221 GLY A 222 149.58 REMARK 500 SER A 410 PRO A 411 -145.70 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 A2019 DISTANCE = 6.19 ANGSTROMS REMARK 525 HOH A2110 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 VSV A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AZI A 1443 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1448 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1450 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO3 A 1451 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1453 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1459 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1505 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2WJP RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH D-GLU CONTAINING REMARK 900 RHODANINE INHIBITOR REMARK 900 RELATED ID: 2VTD RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH D-GLU CONTAINING REMARK 900 SULFONAMIDE INHIBITOR REMARK 900 RELATED ID: 2UUO RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH D-GLU CONTAINING REMARK 900 SULFONAMIDE INHIBITOR 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: 1UAG 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: 2UAG RELATED DB: PDB REMARK 900 UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE 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 900 RELATED ID: 3UAG RELATED DB: PDB REMARK 900 UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE REMARK 900 RELATED ID: 2UUP RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH D-GLU CONTAINING REMARK 900 SULFONAMIDE INHIBITOR REMARK 900 RELATED ID: 1E0D RELATED DB: PDB REMARK 900 UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE REMARK 900 RELATED ID: 2VTE RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH D-GLU CONTAINING REMARK 900 SULFONAMIDE INHIBITOR REMARK 900 RELATED ID: 2JFF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH D-GLU CONTAINING REMARK 900 SULFONAMIDE INHIBITOR REMARK 900 RELATED ID: 1EEH RELATED DB: PDB REMARK 900 UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE DBREF 2X5O A 1 437 UNP P14900 MURD_ECOLI 2 438 SEQADV 2X5O SER A 438 UNP P14900 EXPRESSION TAG SEQADV 2X5O HIS A 439 UNP P14900 EXPRESSION TAG SEQRES 1 A 439 ALA ASP TYR GLN GLY LYS ASN VAL VAL ILE ILE GLY LEU SEQRES 2 A 439 GLY LEU THR GLY LEU SER CYS VAL ASP PHE PHE LEU ALA SEQRES 3 A 439 ARG GLY VAL THR PRO ARG VAL MET ASP THR ARG MET THR SEQRES 4 A 439 PRO PRO GLY LEU ASP LYS LEU PRO GLU ALA VAL GLU ARG SEQRES 5 A 439 HIS THR GLY SER LEU ASN ASP GLU TRP LEU MET ALA ALA SEQRES 6 A 439 ASP LEU ILE VAL ALA SER PRO GLY ILE ALA LEU ALA HIS SEQRES 7 A 439 PRO SER LEU SER ALA ALA ALA ASP ALA GLY ILE GLU ILE SEQRES 8 A 439 VAL GLY ASP ILE GLU LEU PHE CYS ARG GLU ALA GLN ALA SEQRES 9 A 439 PRO ILE VAL ALA ILE THR GLY SER ASN GLY LYS SER THR SEQRES 10 A 439 VAL THR THR LEU VAL GLY GLU MET ALA LYS ALA ALA GLY SEQRES 11 A 439 VAL ASN VAL GLY VAL GLY GLY ASN ILE GLY LEU PRO ALA SEQRES 12 A 439 LEU MET LEU LEU ASP ASP GLU CYS GLU LEU TYR VAL LEU SEQRES 13 A 439 GLU LEU SER SER PHE GLN LEU GLU THR THR SER SER LEU SEQRES 14 A 439 GLN ALA VAL ALA ALA THR ILE LEU ASN VAL THR GLU ASP SEQRES 15 A 439 HIS MET ASP ARG TYR PRO PHE GLY LEU GLN GLN TYR ARG SEQRES 16 A 439 ALA ALA KCX LEU ARG ILE TYR GLU ASN ALA LYS VAL CYS SEQRES 17 A 439 VAL VAL ASN ALA ASP ASP ALA LEU THR MET PRO ILE ARG SEQRES 18 A 439 GLY ALA ASP GLU ARG CYS VAL SER PHE GLY VAL ASN MET SEQRES 19 A 439 GLY ASP TYR HIS LEU ASN HIS GLN GLN GLY GLU THR TRP SEQRES 20 A 439 LEU ARG VAL LYS GLY GLU LYS VAL LEU ASN VAL LYS GLU SEQRES 21 A 439 MET LYS LEU SER GLY GLN HIS ASN TYR THR ASN ALA LEU SEQRES 22 A 439 ALA ALA LEU ALA LEU ALA ASP ALA ALA GLY LEU PRO ARG SEQRES 23 A 439 ALA SER SER LEU LYS ALA LEU THR THR PHE THR GLY LEU SEQRES 24 A 439 PRO HIS ARG PHE GLU VAL VAL LEU GLU HIS ASN GLY VAL SEQRES 25 A 439 ARG TRP ILE ASN ASP SER LYS ALA THR ASN VAL GLY SER SEQRES 26 A 439 THR GLU ALA ALA LEU ASN GLY LEU HIS VAL ASP GLY THR SEQRES 27 A 439 LEU HIS LEU LEU LEU GLY GLY ASP GLY LYS SER ALA ASP SEQRES 28 A 439 PHE SER PRO LEU ALA ARG TYR LEU ASN GLY ASP ASN VAL SEQRES 29 A 439 ARG LEU TYR CYS PHE GLY ARG ASP GLY ALA GLN LEU ALA SEQRES 30 A 439 ALA LEU ARG PRO GLU VAL ALA GLU GLN THR GLU THR MET SEQRES 31 A 439 GLU GLN ALA MET ARG LEU LEU ALA PRO ARG VAL GLN PRO SEQRES 32 A 439 GLY ASP MET VAL LEU LEU SER PRO ALA CYS ALA SER LEU SEQRES 33 A 439 ASP GLN PHE LYS ASN PHE GLU GLN ARG GLY ASN GLU PHE SEQRES 34 A 439 ALA ARG LEU ALA LYS GLU LEU GLY SER HIS MODRES 2X5O KCX A 198 LYS LYSINE NZ-CARBOXYLIC ACID HET KCX A 198 12 HET VSV A 500 34 HET AZI A1443 3 HET SO4 A1448 5 HET SO4 A1450 5 HET SO3 A1451 4 HET CL A1453 1 HET CL A1458 1 HET CL A1459 1 HET CL A1505 1 HETNAM KCX LYSINE NZ-CARBOXYLIC ACID HETNAM VSV N-({3-[({4-[(Z)-(2,4-DIOXO-1,3-THIAZOLIDIN-5-YLIDENE) HETNAM 2 VSV METHYL]PHENYL}AMINO)METHYL]PHENYL}CARBONYL)-D-GLUTAMIC HETNAM 3 VSV ACID HETNAM AZI AZIDE ION HETNAM SO4 SULFATE ION HETNAM SO3 SULFITE ION HETNAM CL CHLORIDE ION FORMUL 1 KCX C7 H14 N2 O4 FORMUL 2 VSV C23 H21 N3 O7 S FORMUL 3 AZI N3 1- FORMUL 4 SO4 2(O4 S 2-) FORMUL 6 SO3 O3 S 2- FORMUL 7 CL 4(CL 1-) FORMUL 11 HOH *535(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 64 1 7 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 1 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 GLN A 242 0 SHEET 2 AC 3 GLU A 245 VAL A 250 -1 O GLU A 245 N GLN A 242 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 2.08 LINK C ALA A 197 N KCX A 198 1555 1555 1.33 LINK C KCX A 198 N LEU A 199 1555 1555 1.32 SITE 1 AC1 20 ASP A 35 THR A 36 ARG A 37 SER A 71 SITE 2 AC1 20 PRO A 72 GLY A 73 PHE A 161 HIS A 183 SITE 3 AC1 20 LYS A 348 ALA A 414 SER A 415 ASN A 421 SITE 4 AC1 20 PHE A 422 HOH A2526 HOH A2527 HOH A2528 SITE 5 AC1 20 HOH A2529 HOH A2530 HOH A2531 HOH A2532 SITE 1 AC2 4 ASP A 417 GLN A 418 PHE A 419 LYS A 420 SITE 1 AC3 8 ASN A 113 GLY A 114 LYS A 115 SER A 116 SITE 2 AC3 8 THR A 117 ARG A 302 HOH A2533 HOH A2534 SITE 1 AC4 3 HIS A 309 ASN A 310 HIS A 439 SITE 1 AC5 5 GLY A 14 LEU A 15 THR A 16 HOH A2033 SITE 2 AC5 5 HOH A2075 SITE 1 AC6 4 ALA A 64 HIS A 309 ASN A 310 HOH A2069 SITE 1 AC7 4 LEU A 191 GLN A 192 GLU A 253 LYS A 254 SITE 1 AC8 1 ASN A 363 CRYST1 66.091 66.091 135.781 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 0.015131 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015131 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007365 0.00000 MASTER 412 0 10 22 20 0 14 6 0 0 0 34 END