HEADER LIGASE 09-DEC-10 2Y1O TITLE DUAL-TARGET INHIBITOR OF MURD AND MURE LIGASES: DESIGN, SYNTHESIS AND TITLE 2 BINDING MODE STUDIES COMPND MOL_ID: 1; COMPND 2 MOLECULE: UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: D-GLUTAMIC ACID-ADDING ENZYME, UDP-N-ACETYLMURAMOYL-L- COMPND 5 ALANYL-D-GLUTAMATE SYNTHETASE, MURD LIGASE; COMPND 6 EC: 6.3.2.9; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 668369; SOURCE 4 STRAIN: DH5[ALPHA]; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 668369; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: DH5[ALPHA]; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PABD16/MURD KEYWDS LIGASE, CELL CYCLE, CELL DIVISION, CELL SHAPE, CELL WALL KEYWDS 2 BIOGENESIS/DEGRADATION EXPDTA X-RAY DIFFRACTION AUTHOR T.TOMASIC,R.SINK,A.KOVAC,S.TURK,C.CONTRERAS-MARTEL,A.DESSEN,D.BLANOT, AUTHOR 2 S.GOBEC,A.ZEGA,D.KIKELJ,L.PETERLIN-MASIC REVDAT 4 20-DEC-23 2Y1O 1 REMARK LINK REVDAT 3 20-DEC-17 2Y1O 1 JRNL REVDAT 2 27-FEB-13 2Y1O 1 JRNL REVDAT 1 28-DEC-11 2Y1O 0 JRNL AUTH T.TOMASIC,R.SINK,N.ZIDAR,A.FIC,C.CONTRERAS-MARTEL,A.DESSEN, JRNL AUTH 2 D.PATIN,D.BLANOT,M.MULLER-PREMRU,S.GOBEC,A.ZEGA,D.KIKELJ, JRNL AUTH 3 L.P.MASIC JRNL TITL DUAL INHIBITOR OF MURD AND MURE LIGASES FROM ESCHERICHIA JRNL TITL 2 COLI AND STAPHYLOCOCCUS AUREUS. JRNL REF ACS MED CHEM LETT V. 3 626 2012 JRNL REFN ISSN 1948-5875 JRNL PMID 24900523 JRNL DOI 10.1021/ML300047H REMARK 2 REMARK 2 RESOLUTION. 1.49 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.56 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 79419 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) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 8826 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) : 1.49 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.53 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3990 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.4800 REMARK 3 BIN FREE R VALUE SET COUNT : 435 REMARK 3 BIN FREE R VALUE : 0.5020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3278 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 70 REMARK 3 SOLVENT ATOMS : 415 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.69 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.54 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.24000 REMARK 3 B22 (A**2) : 0.24000 REMARK 3 B33 (A**2) : -0.48000 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): 0.077 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.077 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.066 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.149 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.955 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3483 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4743 ; 1.612 ; 1.990 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 461 ; 6.544 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 150 ;32.752 ;24.533 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 582 ;12.842 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;18.828 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 546 ; 0.128 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2631 ; 0.007 ; 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): 2203 ; 1.631 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3533 ; 2.505 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1280 ; 3.829 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1196 ; 6.065 ; 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): -27.0057 36.2688 49.0575 REMARK 3 T TENSOR REMARK 3 T11: 0.0232 T22: 0.0410 REMARK 3 T33: 0.0360 T12: 0.0057 REMARK 3 T13: 0.0020 T23: 0.0013 REMARK 3 L TENSOR REMARK 3 L11: 0.5916 L22: 0.7097 REMARK 3 L33: 0.6004 L12: -0.2142 REMARK 3 L13: -0.3760 L23: 0.3499 REMARK 3 S TENSOR REMARK 3 S11: 0.0106 S12: -0.0262 S13: -0.0040 REMARK 3 S21: -0.0123 S22: -0.0007 S23: -0.0142 REMARK 3 S31: -0.0623 S32: -0.0514 S33: -0.0099 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): -4.9319 19.4346 38.4833 REMARK 3 T TENSOR REMARK 3 T11: 0.0328 T22: 0.0563 REMARK 3 T33: 0.0448 T12: 0.0059 REMARK 3 T13: 0.0104 T23: 0.0014 REMARK 3 L TENSOR REMARK 3 L11: 0.3574 L22: 0.1133 REMARK 3 L33: 0.2939 L12: -0.0388 REMARK 3 L13: -0.1988 L23: 0.1603 REMARK 3 S TENSOR REMARK 3 S11: -0.0023 S12: -0.0052 S13: -0.0413 REMARK 3 S21: -0.0081 S22: -0.0062 S23: 0.0025 REMARK 3 S31: 0.0068 S32: 0.0220 S33: 0.0085 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): 8.6422 29.4286 61.0117 REMARK 3 T TENSOR REMARK 3 T11: 0.0024 T22: 0.0546 REMARK 3 T33: 0.0397 T12: -0.0100 REMARK 3 T13: -0.0030 T23: -0.0033 REMARK 3 L TENSOR REMARK 3 L11: 1.2208 L22: 0.5612 REMARK 3 L33: 0.6304 L12: 0.1791 REMARK 3 L13: 0.1457 L23: 0.2363 REMARK 3 S TENSOR REMARK 3 S11: 0.0111 S12: -0.0641 S13: -0.0303 REMARK 3 S21: -0.0075 S22: -0.0232 S23: -0.0338 REMARK 3 S31: -0.0177 S32: -0.0221 S33: 0.0120 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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. U VALUES WITH TLS ADDED. REMARK 4 REMARK 4 2Y1O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-DEC-10. REMARK 100 THE DEPOSITION ID IS D_1290046627. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-APR-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97238 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 : 91441 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.490 REMARK 200 RESOLUTION RANGE LOW (A) : 46.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 82.8 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04000 REMARK 200 FOR THE DATA SET : 27.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 52.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.47000 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 1UAG REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 6.0 MG/ML MURD, 20 MM HEPES, PH 7.4, REMARK 280 200 MM NACL, 5 MM DITHIOTHREITOL, 0.05% (W/V) NAN3 0.1. M HEPES REMARK 280 PH 7.5, 1.9 M AMMONIUM SULPHATE, 7% (W/V) PEG 400, 50 MM NACL 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 67.87350 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 33.93675 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 101.81025 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 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 HIS A 440 REMARK 465 HIS A 441 REMARK 465 HIS A 442 REMARK 465 HIS A 443 REMARK 465 HIS A 444 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 CE MET A 145 O HOH A 2026 2.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 2043 O HOH A 2370 4464 1.91 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 -116.92 -99.09 REMARK 500 GLN A 243 -132.29 60.05 REMARK 500 PHE A 303 52.16 38.76 REMARK 500 ARG A 380 80.23 -161.52 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 A2039 DISTANCE = 6.70 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE T26 A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 600 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1441 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1442 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1444 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1445 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: 2X5O RELATED DB: PDB REMARK 900 DISCOVERY OF NOVEL 5-BENZYLIDENERHODANINE- AND 5-BENZYLIDENE- REMARK 900 THIAZOLIDINE-2,4-DIONE INHIBITORS OF MURD LIGASE REMARK 900 RELATED ID: 1EEH RELATED DB: PDB REMARK 900 UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE DBREF 2Y1O A 0 437 UNP P14900 MURD_ECOLI 1 438 SEQADV 2Y1O SER A 438 UNP P14900 EXPRESSION TAG SEQADV 2Y1O HIS A 439 UNP P14900 EXPRESSION TAG SEQADV 2Y1O HIS A 440 UNP P14900 EXPRESSION TAG SEQADV 2Y1O HIS A 441 UNP P14900 EXPRESSION TAG SEQADV 2Y1O HIS A 442 UNP P14900 EXPRESSION TAG SEQADV 2Y1O HIS A 443 UNP P14900 EXPRESSION TAG SEQADV 2Y1O HIS A 444 UNP P14900 EXPRESSION TAG 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 2Y1O KCX A 198 LYS LYSINE NZ-CARBOXYLIC ACID HET KCX A 198 12 HET T26 A 500 34 HET DMS A 600 4 HET DMS A 601 4 HET DMS A 603 4 HET DMS A 604 4 HET SO4 A1441 5 HET SO4 A1442 5 HET SO4 A1444 5 HET SO4 A1445 5 HETNAM KCX LYSINE NZ-CARBOXYLIC ACID HETNAM T26 (2R)-2-[[3-[[4-[(Z)-(4-OXO-2-SULFANYLIDENE-1,3- HETNAM 2 T26 THIAZOLIDIN-5-YLIDENE) HETNAM 3 T26 METHYL]PHENYL]METHYLAMINO]PHENYL]CARBONYLAMINO]PENTANE HETNAM 4 T26 DIOIC ACID HETNAM DMS DIMETHYL SULFOXIDE HETNAM SO4 SULFATE ION FORMUL 1 KCX C7 H14 N2 O4 FORMUL 2 T26 C23 H21 N3 O6 S2 FORMUL 3 DMS 4(C2 H6 O S) FORMUL 7 SO4 4(O4 S 2-) FORMUL 11 HOH *415(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 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 136 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 2.07 LINK C ALA A 197 N KCX A 198 1555 1555 1.33 LINK C KCX A 198 N LEU A 199 1555 1555 1.33 SITE 1 AC1 24 ILE A 11 ASP A 35 THR A 36 ARG A 37 SITE 2 AC1 24 SER A 71 ILE A 139 PHE A 161 HIS A 183 SITE 3 AC1 24 LYS A 319 ALA A 414 SER A 415 ASN A 421 SITE 4 AC1 24 PHE A 422 DMS A 600 DMS A 603 SO4 A1444 SITE 5 AC1 24 HOH A2402 HOH A2403 HOH A2404 HOH A2405 SITE 6 AC1 24 HOH A2406 HOH A2407 HOH A2408 HOH A2409 SITE 1 AC2 5 GLY A 73 ARG A 186 LEU A 416 T26 A 500 SITE 2 AC2 5 HOH A2409 SITE 1 AC3 7 LEU A 163 THR A 166 SER A 167 SER A 168 SITE 2 AC3 7 LEU A 169 ARG A 200 GLU A 203 SITE 1 AC4 5 PRO A 72 SER A 159 GLN A 162 T26 A 500 SITE 2 AC4 5 HOH A2180 SITE 1 AC5 6 ASN A 7 ALA A 64 HIS A 309 ASN A 310 SITE 2 AC5 6 HOH A2094 HOH A2410 SITE 1 AC6 9 ASN A 113 GLY A 114 LYS A 115 SER A 116 SITE 2 AC6 9 THR A 117 ARG A 302 LYS A 319 HOH A2411 SITE 3 AC6 9 HOH A2412 SITE 1 AC7 4 HIS A 309 ASN A 310 SER A 438 HIS A 439 SITE 1 AC8 6 GLY A 14 LEU A 15 THR A 16 ILE A 139 SITE 2 AC8 6 T26 A 500 HOH A2413 SITE 1 AC9 4 ARG A 37 MET A 38 GLN A 170 HOH A2415 CRYST1 65.844 65.844 135.747 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 0.015187 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015187 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007367 0.00000