HEADER ISOMERASE 25-NOV-08 2W4I TITLE CRYSTAL STRUCTURE OF HELICOBACTER PYLORI GLUTAMATE RACEMASE IN COMPLEX TITLE 2 WITH D-GLUTAMATE AND AN INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAMATE RACEMASE; COMPND 3 CHAIN: A, B, E, F; COMPND 4 EC: 5.1.1.3; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI; SOURCE 3 ORGANISM_TAXID: 210; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ISOMERASE, CELL SHAPE, GLUTAMATE RACEMASE, CELL WALL KEYWDS 2 BIOGENESIS/DEGRADATION, PEPTIDOGLYCAN SYNTHESIS, PEPTIDOGLYCAN KEYWDS 3 BIOSYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR T.LUNDQVIST REVDAT 5 13-DEC-23 2W4I 1 REMARK REVDAT 4 04-MAR-20 2W4I 1 REMARK REVDAT 3 09-AUG-17 2W4I 1 JRNL REMARK REVDAT 2 03-FEB-09 2W4I 1 JRNL REMARK REVDAT 1 09-DEC-08 2W4I 0 JRNL AUTH B.GENG,G.BASARAB,J.COMITA-PREVOIR,M.GOWRAVARAM,P.HILL, JRNL AUTH 2 A.KIELY,J.LOCH,L.MACPHERSON,M.MORNINGSTAR,G.MULLEN, JRNL AUTH 3 E.OSIMBONI,A.SATZ,C.EYERMANN,T.LUNDQVIST JRNL TITL POTENT AND SELECTIVE INHIBITORS OF HELICOBACTER PYLORI JRNL TITL 2 GLUTAMATE RACEMASE (MURI): PYRIDODIAZEPINE AMINES. JRNL REF BIOORG. MED. CHEM. LETT. V. 19 930 2009 JRNL REFN ESSN 1464-3405 JRNL PMID 19097892 JRNL DOI 10.1016/J.BMCL.2008.11.113 REMARK 2 REMARK 2 RESOLUTION. 1.87 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.87 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.67 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 84479 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) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4456 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) : 1.87 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.92 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5824 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1980 REMARK 3 BIN FREE R VALUE SET COUNT : 286 REMARK 3 BIN FREE R VALUE : 0.2570 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 8021 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 94 REMARK 3 SOLVENT ATOMS : 1351 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.59 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : 0.05000 REMARK 3 B33 (A**2) : -0.03000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.01000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.134 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.133 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.082 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.642 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.928 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 8311 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 11281 ; 1.352 ; 1.994 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 1013 ; 5.450 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 332 ;40.328 ;25.060 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1442 ;13.262 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;18.523 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1290 ; 0.095 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6162 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 4522 ; 0.207 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 5793 ; 0.309 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 1108 ; 0.169 ; 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): 104 ; 0.199 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 86 ; 0.214 ; 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): 5284 ; 0.881 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 8250 ; 1.372 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3479 ; 2.302 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3027 ; 3.726 ; 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2W4I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-NOV-08. REMARK 100 THE DEPOSITION ID IS D_1290038189. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-SEP-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX II REMARK 200 BEAMLINE : I711 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.089 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 210077 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.870 REMARK 200 RESOLUTION RANGE LOW (A) : 25.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.87 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.20000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.800 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: PDB ENTRY 2JFZ REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM TRIS PH 8, NAAC 150 MM, 15% REMARK 280 GLYCEROL, PEG 3350 20-35% REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z 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 46.99100 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F 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 LEU B 255 REMARK 465 LEU E 255 REMARK 465 LEU F 255 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 B 2161 O HOH B 2285 1.94 REMARK 500 O HOH F 2145 O HOH F 2147 2.11 REMARK 500 NE2 GLN B 219 O HOH B 2287 2.12 REMARK 500 O HOH B 2134 O HOH B 2138 2.13 REMARK 500 O HOH F 2002 O HOH F 2003 2.19 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 B 2004 O HOH F 2003 2546 2.12 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 ILE A 93 -61.06 -90.16 REMARK 500 ASN A 123 18.94 57.60 REMARK 500 PHE A 231 119.26 -164.95 REMARK 500 ALA B 200 63.14 60.36 REMARK 500 ASN E 123 19.55 49.79 REMARK 500 ASN E 227 38.44 -145.26 REMARK 500 ASN F 226 53.75 -91.94 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 A2006 DISTANCE = 6.52 ANGSTROMS REMARK 525 HOH A2047 DISTANCE = 6.10 ANGSTROMS REMARK 525 HOH A2059 DISTANCE = 6.20 ANGSTROMS REMARK 525 HOH A2115 DISTANCE = 5.83 ANGSTROMS REMARK 525 HOH B2010 DISTANCE = 6.06 ANGSTROMS REMARK 525 HOH E2003 DISTANCE = 5.90 ANGSTROMS REMARK 525 HOH F2045 DISTANCE = 6.66 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DGL A1256 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DGL B1255 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DGL E1255 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DGL F1255 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE VGA B1256 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE VGA E1256 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2JFZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HELICOBACTER PYLORI GLUTAMATE RACEMASE IN REMARK 900 COMPLEX WITH D- GLUTAMATE AND AN INHIBITOR REMARK 900 RELATED ID: 2JFX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HELICOBACTER PYLORI GLUTAMATE RACEMASE IN REMARK 900 COMPLEX WITH D- GLUTAMATE REMARK 900 RELATED ID: 2JFY RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HELICOBACTER PYLORI GLUTAMATE RACEMASE IN REMARK 900 COMPLEX WITH D- GLUTAMATE DBREF 2W4I A 1 255 UNP Q9ZLT0 MURI_HELPJ 1 255 DBREF 2W4I B 1 255 UNP Q9ZLT0 MURI_HELPJ 1 255 DBREF 2W4I E 1 255 UNP Q9ZLT0 MURI_HELPJ 1 255 DBREF 2W4I F 1 255 UNP Q9ZLT0 MURI_HELPJ 1 255 SEQRES 1 A 255 MET LYS ILE GLY VAL PHE ASP SER GLY VAL GLY GLY PHE SEQRES 2 A 255 SER VAL LEU LYS SER LEU LEU LYS ALA ARG LEU PHE ASP SEQRES 3 A 255 GLU ILE ILE TYR TYR GLY ASP SER ALA ARG VAL PRO TYR SEQRES 4 A 255 GLY THR LYS ASP PRO THR THR ILE LYS GLN PHE GLY LEU SEQRES 5 A 255 GLU ALA LEU ASP PHE PHE LYS PRO HIS GLU ILE GLU LEU SEQRES 6 A 255 LEU ILE VAL ALA CYS ASN THR ALA SER ALA LEU ALA LEU SEQRES 7 A 255 GLU GLU MET GLN LYS TYR SER LYS ILE PRO ILE VAL GLY SEQRES 8 A 255 VAL ILE GLU PRO SER ILE LEU ALA ILE LYS ARG GLN VAL SEQRES 9 A 255 GLU ASP LYS ASN ALA PRO ILE LEU VAL LEU GLY THR LYS SEQRES 10 A 255 ALA THR ILE GLN SER ASN ALA TYR ASP ASN ALA LEU LYS SEQRES 11 A 255 GLN GLN GLY TYR LEU ASN ILE SER HIS LEU ALA THR SER SEQRES 12 A 255 LEU PHE VAL PRO LEU ILE GLU GLU SER ILE LEU GLU GLY SEQRES 13 A 255 GLU LEU LEU GLU THR CYS MET HIS TYR TYR PHE THR PRO SEQRES 14 A 255 LEU GLU ILE LEU PRO GLU VAL ILE ILE LEU GLY CYS THR SEQRES 15 A 255 HIS PHE PRO LEU ILE ALA GLN LYS ILE GLU GLY TYR PHE SEQRES 16 A 255 MET GLY HIS PHE ALA LEU PRO THR PRO PRO LEU LEU ILE SEQRES 17 A 255 HIS SER GLY ASP ALA ILE VAL GLU TYR LEU GLN GLN LYS SEQRES 18 A 255 TYR ALA LEU LYS ASN ASN ALA CYS THR PHE PRO LYS VAL SEQRES 19 A 255 GLU PHE HIS ALA SER GLY ASP VAL ILE TRP LEU GLU ARG SEQRES 20 A 255 GLN ALA LYS GLU TRP LEU LYS LEU SEQRES 1 B 255 MET LYS ILE GLY VAL PHE ASP SER GLY VAL GLY GLY PHE SEQRES 2 B 255 SER VAL LEU LYS SER LEU LEU LYS ALA ARG LEU PHE ASP SEQRES 3 B 255 GLU ILE ILE TYR TYR GLY ASP SER ALA ARG VAL PRO TYR SEQRES 4 B 255 GLY THR LYS ASP PRO THR THR ILE LYS GLN PHE GLY LEU SEQRES 5 B 255 GLU ALA LEU ASP PHE PHE LYS PRO HIS GLU ILE GLU LEU SEQRES 6 B 255 LEU ILE VAL ALA CYS ASN THR ALA SER ALA LEU ALA LEU SEQRES 7 B 255 GLU GLU MET GLN LYS TYR SER LYS ILE PRO ILE VAL GLY SEQRES 8 B 255 VAL ILE GLU PRO SER ILE LEU ALA ILE LYS ARG GLN VAL SEQRES 9 B 255 GLU ASP LYS ASN ALA PRO ILE LEU VAL LEU GLY THR LYS SEQRES 10 B 255 ALA THR ILE GLN SER ASN ALA TYR ASP ASN ALA LEU LYS SEQRES 11 B 255 GLN GLN GLY TYR LEU ASN ILE SER HIS LEU ALA THR SER SEQRES 12 B 255 LEU PHE VAL PRO LEU ILE GLU GLU SER ILE LEU GLU GLY SEQRES 13 B 255 GLU LEU LEU GLU THR CYS MET HIS TYR TYR PHE THR PRO SEQRES 14 B 255 LEU GLU ILE LEU PRO GLU VAL ILE ILE LEU GLY CYS THR SEQRES 15 B 255 HIS PHE PRO LEU ILE ALA GLN LYS ILE GLU GLY TYR PHE SEQRES 16 B 255 MET GLY HIS PHE ALA LEU PRO THR PRO PRO LEU LEU ILE SEQRES 17 B 255 HIS SER GLY ASP ALA ILE VAL GLU TYR LEU GLN GLN LYS SEQRES 18 B 255 TYR ALA LEU LYS ASN ASN ALA CYS THR PHE PRO LYS VAL SEQRES 19 B 255 GLU PHE HIS ALA SER GLY ASP VAL ILE TRP LEU GLU ARG SEQRES 20 B 255 GLN ALA LYS GLU TRP LEU LYS LEU SEQRES 1 E 255 MET LYS ILE GLY VAL PHE ASP SER GLY VAL GLY GLY PHE SEQRES 2 E 255 SER VAL LEU LYS SER LEU LEU LYS ALA ARG LEU PHE ASP SEQRES 3 E 255 GLU ILE ILE TYR TYR GLY ASP SER ALA ARG VAL PRO TYR SEQRES 4 E 255 GLY THR LYS ASP PRO THR THR ILE LYS GLN PHE GLY LEU SEQRES 5 E 255 GLU ALA LEU ASP PHE PHE LYS PRO HIS GLU ILE GLU LEU SEQRES 6 E 255 LEU ILE VAL ALA CYS ASN THR ALA SER ALA LEU ALA LEU SEQRES 7 E 255 GLU GLU MET GLN LYS TYR SER LYS ILE PRO ILE VAL GLY SEQRES 8 E 255 VAL ILE GLU PRO SER ILE LEU ALA ILE LYS ARG GLN VAL SEQRES 9 E 255 GLU ASP LYS ASN ALA PRO ILE LEU VAL LEU GLY THR LYS SEQRES 10 E 255 ALA THR ILE GLN SER ASN ALA TYR ASP ASN ALA LEU LYS SEQRES 11 E 255 GLN GLN GLY TYR LEU ASN ILE SER HIS LEU ALA THR SER SEQRES 12 E 255 LEU PHE VAL PRO LEU ILE GLU GLU SER ILE LEU GLU GLY SEQRES 13 E 255 GLU LEU LEU GLU THR CYS MET HIS TYR TYR PHE THR PRO SEQRES 14 E 255 LEU GLU ILE LEU PRO GLU VAL ILE ILE LEU GLY CYS THR SEQRES 15 E 255 HIS PHE PRO LEU ILE ALA GLN LYS ILE GLU GLY TYR PHE SEQRES 16 E 255 MET GLY HIS PHE ALA LEU PRO THR PRO PRO LEU LEU ILE SEQRES 17 E 255 HIS SER GLY ASP ALA ILE VAL GLU TYR LEU GLN GLN LYS SEQRES 18 E 255 TYR ALA LEU LYS ASN ASN ALA CYS THR PHE PRO LYS VAL SEQRES 19 E 255 GLU PHE HIS ALA SER GLY ASP VAL ILE TRP LEU GLU ARG SEQRES 20 E 255 GLN ALA LYS GLU TRP LEU LYS LEU SEQRES 1 F 255 MET LYS ILE GLY VAL PHE ASP SER GLY VAL GLY GLY PHE SEQRES 2 F 255 SER VAL LEU LYS SER LEU LEU LYS ALA ARG LEU PHE ASP SEQRES 3 F 255 GLU ILE ILE TYR TYR GLY ASP SER ALA ARG VAL PRO TYR SEQRES 4 F 255 GLY THR LYS ASP PRO THR THR ILE LYS GLN PHE GLY LEU SEQRES 5 F 255 GLU ALA LEU ASP PHE PHE LYS PRO HIS GLU ILE GLU LEU SEQRES 6 F 255 LEU ILE VAL ALA CYS ASN THR ALA SER ALA LEU ALA LEU SEQRES 7 F 255 GLU GLU MET GLN LYS TYR SER LYS ILE PRO ILE VAL GLY SEQRES 8 F 255 VAL ILE GLU PRO SER ILE LEU ALA ILE LYS ARG GLN VAL SEQRES 9 F 255 GLU ASP LYS ASN ALA PRO ILE LEU VAL LEU GLY THR LYS SEQRES 10 F 255 ALA THR ILE GLN SER ASN ALA TYR ASP ASN ALA LEU LYS SEQRES 11 F 255 GLN GLN GLY TYR LEU ASN ILE SER HIS LEU ALA THR SER SEQRES 12 F 255 LEU PHE VAL PRO LEU ILE GLU GLU SER ILE LEU GLU GLY SEQRES 13 F 255 GLU LEU LEU GLU THR CYS MET HIS TYR TYR PHE THR PRO SEQRES 14 F 255 LEU GLU ILE LEU PRO GLU VAL ILE ILE LEU GLY CYS THR SEQRES 15 F 255 HIS PHE PRO LEU ILE ALA GLN LYS ILE GLU GLY TYR PHE SEQRES 16 F 255 MET GLY HIS PHE ALA LEU PRO THR PRO PRO LEU LEU ILE SEQRES 17 F 255 HIS SER GLY ASP ALA ILE VAL GLU TYR LEU GLN GLN LYS SEQRES 18 F 255 TYR ALA LEU LYS ASN ASN ALA CYS THR PHE PRO LYS VAL SEQRES 19 F 255 GLU PHE HIS ALA SER GLY ASP VAL ILE TRP LEU GLU ARG SEQRES 20 F 255 GLN ALA LYS GLU TRP LEU LYS LEU HET DGL A1256 10 HET DGL B1255 10 HET VGA B1256 27 HET DGL E1255 10 HET VGA E1256 27 HET DGL F1255 10 HETNAM DGL D-GLUTAMIC ACID HETNAM VGA 1-[(3S)-5-PHENYL-3-THIOPHEN-2-YL-3H-1,4-BENZODIAZEPIN- HETNAM 2 VGA 2-YL]AZETIDIN-3-OL FORMUL 5 DGL 4(C5 H9 N O4) FORMUL 7 VGA 2(C22 H19 N3 O S) FORMUL 11 HOH *1351(H2 O) HELIX 1 1 GLY A 12 ARG A 23 1 12 HELIX 2 2 ASP A 43 LYS A 59 1 17 HELIX 3 3 PRO A 60 GLU A 62 5 3 HELIX 4 4 CYS A 70 ALA A 77 1 8 HELIX 5 5 ALA A 77 TYR A 84 1 8 HELIX 6 6 ILE A 93 VAL A 104 1 12 HELIX 7 7 THR A 116 ASN A 123 1 8 HELIX 8 8 ASN A 123 GLN A 132 1 10 HELIX 9 9 LEU A 144 GLU A 151 1 8 HELIX 10 10 GLU A 155 THR A 168 1 14 HELIX 11 11 HIS A 183 LEU A 186 5 4 HELIX 12 12 ILE A 187 ALA A 200 1 14 HELIX 13 13 SER A 210 TYR A 222 1 13 HELIX 14 14 ALA A 223 ASN A 226 5 4 HELIX 15 15 ASP A 241 LYS A 254 1 14 HELIX 16 16 GLY B 12 ARG B 23 1 12 HELIX 17 17 ASP B 43 LYS B 59 1 17 HELIX 18 18 PRO B 60 GLU B 62 5 3 HELIX 19 19 CYS B 70 SER B 85 1 16 HELIX 20 20 VAL B 92 VAL B 104 1 13 HELIX 21 21 THR B 116 SER B 122 1 7 HELIX 22 22 ASN B 123 GLN B 132 1 10 HELIX 23 23 LEU B 144 GLU B 151 1 8 HELIX 24 24 GLU B 155 THR B 168 1 14 HELIX 25 25 HIS B 183 LEU B 186 5 4 HELIX 26 26 ILE B 187 ALA B 200 1 14 HELIX 27 27 SER B 210 TYR B 222 1 13 HELIX 28 28 ASP B 241 LYS B 254 1 14 HELIX 29 29 GLY E 12 ARG E 23 1 12 HELIX 30 30 ASP E 43 LYS E 59 1 17 HELIX 31 31 PRO E 60 GLU E 62 5 3 HELIX 32 32 CYS E 70 ALA E 77 1 8 HELIX 33 33 ALA E 77 TYR E 84 1 8 HELIX 34 34 VAL E 92 VAL E 104 1 13 HELIX 35 35 THR E 116 SER E 122 1 7 HELIX 36 36 ASN E 123 GLN E 132 1 10 HELIX 37 37 LEU E 144 GLU E 151 1 8 HELIX 38 38 GLU E 155 THR E 168 1 14 HELIX 39 39 HIS E 183 LEU E 186 5 4 HELIX 40 40 ILE E 187 PHE E 199 1 13 HELIX 41 41 SER E 210 TYR E 222 1 13 HELIX 42 42 ASP E 241 LEU E 253 1 13 HELIX 43 43 GLY F 12 ALA F 22 1 11 HELIX 44 44 ASP F 43 LYS F 59 1 17 HELIX 45 45 PRO F 60 GLU F 62 5 3 HELIX 46 46 CYS F 70 TYR F 84 1 15 HELIX 47 47 VAL F 92 VAL F 104 1 13 HELIX 48 48 THR F 116 ASN F 123 1 8 HELIX 49 49 ASN F 123 GLN F 132 1 10 HELIX 50 50 LEU F 144 GLU F 151 1 8 HELIX 51 51 GLU F 155 THR F 168 1 14 HELIX 52 52 HIS F 183 LEU F 186 5 4 HELIX 53 53 ILE F 187 PHE F 199 1 13 HELIX 54 54 SER F 210 TYR F 222 1 13 HELIX 55 55 ASP F 241 LEU F 253 1 13 SHEET 1 AA 5 ILE A 89 GLY A 91 0 SHEET 2 AA 5 LEU A 66 VAL A 68 1 O LEU A 66 N VAL A 90 SHEET 3 AA 5 LYS A 2 ASP A 7 1 O GLY A 4 N ILE A 67 SHEET 4 AA 5 GLU A 27 GLY A 32 1 O GLU A 27 N ILE A 3 SHEET 5 AA 5 LYS A 233 ALA A 238 1 O LYS A 233 N ILE A 28 SHEET 1 AB 4 ILE A 137 ALA A 141 0 SHEET 2 AB 4 ILE A 111 GLY A 115 1 O ILE A 111 N SER A 138 SHEET 3 AB 4 VAL A 176 GLY A 180 1 O VAL A 176 N LEU A 112 SHEET 4 AB 4 LEU A 206 HIS A 209 1 O LEU A 206 N ILE A 177 SHEET 1 BA 5 ILE B 89 VAL B 90 0 SHEET 2 BA 5 LEU B 65 VAL B 68 1 O LEU B 66 N VAL B 90 SHEET 3 BA 5 LYS B 2 ASP B 7 1 O GLY B 4 N ILE B 67 SHEET 4 BA 5 GLU B 27 GLY B 32 1 O GLU B 27 N ILE B 3 SHEET 5 BA 5 LYS B 233 ALA B 238 1 O LYS B 233 N ILE B 28 SHEET 1 BB 4 ILE B 137 ALA B 141 0 SHEET 2 BB 4 ILE B 111 GLY B 115 1 O ILE B 111 N SER B 138 SHEET 3 BB 4 VAL B 176 GLY B 180 1 O VAL B 176 N LEU B 112 SHEET 4 BB 4 LEU B 206 HIS B 209 1 O LEU B 206 N ILE B 177 SHEET 1 EA 5 ILE E 89 GLY E 91 0 SHEET 2 EA 5 LEU E 66 VAL E 68 1 O LEU E 66 N VAL E 90 SHEET 3 EA 5 LYS E 2 ASP E 7 1 O GLY E 4 N ILE E 67 SHEET 4 EA 5 GLU E 27 GLY E 32 1 O GLU E 27 N ILE E 3 SHEET 5 EA 5 LYS E 233 ALA E 238 1 O LYS E 233 N ILE E 28 SHEET 1 EB 4 ILE E 137 ALA E 141 0 SHEET 2 EB 4 ILE E 111 GLY E 115 1 O ILE E 111 N SER E 138 SHEET 3 EB 4 VAL E 176 LEU E 179 1 O VAL E 176 N LEU E 112 SHEET 4 EB 4 LEU E 206 HIS E 209 1 O LEU E 206 N ILE E 177 SHEET 1 FA 5 ILE F 89 VAL F 90 0 SHEET 2 FA 5 LEU F 65 VAL F 68 1 O LEU F 66 N VAL F 90 SHEET 3 FA 5 LYS F 2 ASP F 7 1 O GLY F 4 N ILE F 67 SHEET 4 FA 5 GLU F 27 GLY F 32 1 O GLU F 27 N ILE F 3 SHEET 5 FA 5 LYS F 233 ALA F 238 1 O LYS F 233 N ILE F 28 SHEET 1 FB 4 ILE F 137 ALA F 141 0 SHEET 2 FB 4 ILE F 111 GLY F 115 1 O ILE F 111 N SER F 138 SHEET 3 FB 4 VAL F 176 GLY F 180 1 O VAL F 176 N LEU F 112 SHEET 4 FB 4 LEU F 206 HIS F 209 1 O LEU F 206 N ILE F 177 CISPEP 1 VAL A 37 PRO A 38 0 3.30 CISPEP 2 VAL B 37 PRO B 38 0 1.63 CISPEP 3 VAL E 37 PRO E 38 0 3.74 CISPEP 4 VAL F 37 PRO F 38 0 -1.29 SITE 1 AC1 14 ASP A 7 SER A 8 PRO A 38 TYR A 39 SITE 2 AC1 14 GLY A 40 CYS A 70 ASN A 71 THR A 72 SITE 3 AC1 14 THR A 116 CYS A 181 THR A 182 HOH A2007 SITE 4 AC1 14 HOH A2294 HOH A2393 SITE 1 AC2 14 ASP B 7 SER B 8 PRO B 38 TYR B 39 SITE 2 AC2 14 GLY B 40 CYS B 70 ASN B 71 THR B 72 SITE 3 AC2 14 THR B 116 CYS B 181 THR B 182 HOH B2007 SITE 4 AC2 14 HOH B2264 HOH B2328 SITE 1 AC3 14 ASP E 7 SER E 8 PRO E 38 TYR E 39 SITE 2 AC3 14 GLY E 40 CYS E 70 ASN E 71 THR E 72 SITE 3 AC3 14 THR E 116 CYS E 181 THR E 182 HIS E 183 SITE 4 AC3 14 HOH E2325 HOH E2326 SITE 1 AC4 13 ASP F 7 SER F 8 PRO F 38 TYR F 39 SITE 2 AC4 13 GLY F 40 CYS F 70 ASN F 71 THR F 72 SITE 3 AC4 13 THR F 116 CYS F 181 THR F 182 HOH F2243 SITE 4 AC4 13 HOH F2307 SITE 1 AC5 17 PRO A 38 THR A 41 SER A 143 VAL A 146 SITE 2 AC5 17 PRO A 147 GLU A 150 GLU A 151 HOH A2244 SITE 3 AC5 17 PRO B 38 THR B 41 LYS B 117 VAL B 146 SITE 4 AC5 17 PRO B 147 GLU B 150 GLU B 151 HOH B2214 SITE 5 AC5 17 HOH B2329 SITE 1 AC6 13 THR E 41 SER E 143 VAL E 146 PRO E 147 SITE 2 AC6 13 GLU E 150 GLU E 151 HOH E2327 HOH E2328 SITE 3 AC6 13 PRO F 38 VAL F 146 PRO F 147 GLU F 150 SITE 4 AC6 13 GLU F 151 CRYST1 59.074 93.982 101.295 90.00 91.46 90.00 P 1 21 1 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 0.016928 0.000000 0.000431 0.00000 SCALE2 0.000000 0.010640 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009875 0.00000