HEADER LYASE 14-AUG-12 4B6S TITLE STRUCTURE OF HELICOBACTER PYLORI TYPE II DEHYDROQUINASE INHIBITED BY TITLE 2 (2S)-2-PERFLUOROBENZYL-3-DEHYDROQUINIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3-DEHYDROQUINATE DEHYDRATASE; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: 3-DEHYDROQUINASE, TYPE II DHQASE; COMPND 5 EC: 4.2.1.10; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI 26695; SOURCE 3 ORGANISM_TAXID: 85962; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET21A KEYWDS LYASE EXPDTA X-RAY DIFFRACTION AUTHOR J.M.OTERO,A.L.LLAMAS-SAIZ,E.LENCE,L.TIZON,A.PEON,V.F.V.PRAZERES, AUTHOR 2 H.LAMB,A.R.HAWKINS,C.GONZALEZ-BELLO,M.J.VAN RAAIJ REVDAT 6 20-DEC-23 4B6S 1 REMARK REVDAT 5 17-JAN-18 4B6S 1 JRNL REVDAT 4 07-AUG-13 4B6S 1 HETNAM HETSYN REVDAT 3 27-MAR-13 4B6S 1 JRNL REVDAT 2 20-MAR-13 4B6S 1 TITLE REMARK REVDAT 1 19-DEC-12 4B6S 0 JRNL AUTH E.LENCE,L.TIZON,J.M.OTERO,A.PEON,V.F.PRAZERES, JRNL AUTH 2 A.L.LLAMAS-SAIZ,G.C.FOX,M.J.VAN RAAIJ,H.LAMB,A.R.HAWKINS, JRNL AUTH 3 C.GONZALEZ-BELLO JRNL TITL MECHANISTIC BASIS OF THE INHIBITION OF TYPE II JRNL TITL 2 DEHYDROQUINASE BY (2S)- AND (2R)-2-BENZYL-3-DEHYDROQUINIC JRNL TITL 3 ACIDS. JRNL REF ACS CHEM. BIOL. V. 8 568 2013 JRNL REFN ESSN 1554-8937 JRNL PMID 23198883 JRNL DOI 10.1021/CB300493S REMARK 2 REMARK 2 RESOLUTION. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 58.65 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 41125 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : THIN SHELLS REMARK 3 R VALUE (WORKING + TEST SET) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1180 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6017 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.98 REMARK 3 BIN R VALUE (WORKING SET) : 0.3850 REMARK 3 BIN FREE R VALUE SET COUNT : 21 REMARK 3 BIN FREE R VALUE : 0.4150 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3638 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 80 REMARK 3 SOLVENT ATOMS : 236 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.31 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.72000 REMARK 3 B22 (A**2) : -0.72000 REMARK 3 B33 (A**2) : 1.45000 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): 0.173 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.167 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.130 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.548 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.896 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3817 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5164 ; 1.500 ; 1.978 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 468 ; 6.736 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 178 ;37.026 ;25.955 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 682 ;16.666 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;13.451 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 579 ; 0.107 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2860 ; 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): 2330 ; 1.014 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3751 ; 1.767 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1487 ; 2.328 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1413 ; 3.512 ; 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. U VALUES REFINED INDIVIDUALLY REMARK 4 REMARK 4 4B6S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1290053744. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUL-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98011 REMARK 200 MONOCHROMATOR : CHANNEL CUT CRYOGENICALLY COOLED REMARK 200 MONOCHROMATOR CRYSTAL REMARK 200 OPTICS : KIRKPATRICK-BAEZ PAIR OF BI REMARK 200 -MORPH MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42501 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 58.650 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.800 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.29000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 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 2C4V REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM TRIS-HCL PH 7.5, 1 MM 2 REMARK 280 -MERCAPTOETHANOL, 1 MM ETHYLENEDIAMINETETRAACETIC ACID, 200 MM REMARK 280 SODIUM CHLORIDE, 32% (W/V) POLYETHYLENEGLYCOL 4000, 0.1 M SODIUM REMARK 280 CITRATE PH 5.4 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y,X,Z+1/2 REMARK 290 4555 Y,-X,Z+1/2 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z REMARK 290 7555 Y,X,-Z+1/2 REMARK 290 8555 -Y,-X,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 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 52.29000 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 52.29000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 52.29000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 52.29000 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: DODECAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DODECAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 28010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 72950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -218.4 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 100.19000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 -1.000000 0.000000 100.19000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2039 LIES ON A SPECIAL POSITION. 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 PRO A 159 REMARK 465 ASN A 160 REMARK 465 ASN A 161 REMARK 465 PRO A 162 REMARK 465 ILE A 163 REMARK 465 ASN A 164 REMARK 465 ASN A 165 REMARK 465 GLN A 166 REMARK 465 LYS A 167 REMARK 465 PRO B 159 REMARK 465 ASN B 160 REMARK 465 ASN B 161 REMARK 465 PRO B 162 REMARK 465 ILE B 163 REMARK 465 ASN B 164 REMARK 465 ASN B 165 REMARK 465 GLN B 166 REMARK 465 LYS B 167 REMARK 465 LYS C 156 REMARK 465 ASN C 157 REMARK 465 ASN C 158 REMARK 465 PRO C 159 REMARK 465 ASN C 160 REMARK 465 ASN C 161 REMARK 465 PRO C 162 REMARK 465 ILE C 163 REMARK 465 ASN C 164 REMARK 465 ASN C 165 REMARK 465 GLN C 166 REMARK 465 LYS C 167 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 ARG C 17 O HOH C 2005 2.12 REMARK 500 OE1 GLN C 35 O HOH C 2014 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG B 113 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES 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 ASN A 10 -6.72 74.68 REMARK 500 ARG A 17 150.81 179.54 REMARK 500 ARG A 20 -71.59 -69.89 REMARK 500 TYR A 22 -158.64 -101.63 REMARK 500 ASN A 42 54.69 39.89 REMARK 500 ARG A 109 -149.89 -128.34 REMARK 500 ASN B 10 -1.47 72.97 REMARK 500 ARG B 17 157.59 122.23 REMARK 500 ASP B 18 62.48 80.29 REMARK 500 ARG B 109 -152.71 -127.47 REMARK 500 ASN C 10 -5.06 72.36 REMARK 500 HIS C 16 4.56 -64.78 REMARK 500 ARG C 17 166.45 142.95 REMARK 500 ASP C 18 57.07 75.76 REMARK 500 LEU C 21 -17.49 -156.70 REMARK 500 ARG C 109 -143.67 -125.08 REMARK 500 GLN C 152 -74.40 -69.37 REMARK 500 ALA C 154 46.04 -73.75 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 B 17 ASP B 18 -147.55 REMARK 500 HIS C 16 ARG C 17 144.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2HN A 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2HN B 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2HN C 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 1159 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1J2Y RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE TYPE II 3-DEHYDROQUINASE REMARK 900 RELATED ID: 2C4V RELATED DB: PDB REMARK 900 H. PYLORI TYPE II DHQASE IN COMPLEX WITH CITRATE REMARK 900 RELATED ID: 2C4W RELATED DB: PDB REMARK 900 TYPE II DEHYDROQUINASE FROM H. PYLORI IN COMPLEX WITH AH9095 REMARK 900 RELATED ID: 2C57 RELATED DB: PDB REMARK 900 H.PYLORI TYPE II DEHYDROQUINASE IN COMPLEX WITH FA1 REMARK 900 RELATED ID: 2WKS RELATED DB: PDB REMARK 900 STRUCTURE OF HELICOBACTER PYLORI TYPE II DEHYDROQUINASE WITH A NEW REMARK 900 CARBASUGAR-THIOPHENE INHIBITOR. REMARK 900 RELATED ID: 2XB9 RELATED DB: PDB REMARK 900 STRUCTURE OF HELICOBACTER PYLORI TYPE II DEHYDROQUINASE IN COMPLEX REMARK 900 WITH INHIBITOR COMPOUND (2R)-2-(4- METHOXYBENZYL)-3-DEHYDROQUINIC REMARK 900 ACID REMARK 900 RELATED ID: 2XD9 RELATED DB: PDB REMARK 900 STRUCTURE OF HELICOBACTER PYLORI TYPE II DEHYDROQUINASE IN COMPLEX REMARK 900 WITH INHIBITOR COMPOUND (4R,6R,7S)-4,6, 7-TRIHYDROXY-2-((E)-PROP-1- REMARK 900 ENYL)-4,5,6,7- TETRAHYDROBENZO(B)THIOPHENE-4-CARBOXYLIC ACID REMARK 900 RELATED ID: 2XDA RELATED DB: PDB REMARK 900 STRUCTURE OF HELICOBACTER PYLORI TYPE II DEHYDROQUINASE IN COMPLEX REMARK 900 WITH INHIBITOR COMPOUND (4R,6R,7S)-2-(2- CYCLOPROPYL)ETHYL-4,6,7- REMARK 900 TRIHYDROXY-4,5,6,7- TETRAHYDROBENZO(B)THIOPHENE-4-CARBOXYLIC ACID REMARK 900 RELATED ID: 4B6R RELATED DB: PDB REMARK 900 STRUCTURE OF HELICOBACTER PYLORI TYPE II DEHYDROQUINASE INHIBITED REMARK 900 BY (2S)-2-(4-METHOXY)BENZYL-3 -DEHYDROQUINIC ACID DBREF 4B6S A 1 167 UNP Q48255 AROQ_HELPY 1 167 DBREF 4B6S B 1 167 UNP Q48255 AROQ_HELPY 1 167 DBREF 4B6S C 1 167 UNP Q48255 AROQ_HELPY 1 167 SEQRES 1 A 167 MET LYS ILE LEU VAL ILE GLN GLY PRO ASN LEU ASN MET SEQRES 2 A 167 LEU GLY HIS ARG ASP PRO ARG LEU TYR GLY MET VAL THR SEQRES 3 A 167 LEU ASP GLN ILE HIS GLU ILE MET GLN THR PHE VAL LYS SEQRES 4 A 167 GLN GLY ASN LEU ASP VAL GLU LEU GLU PHE PHE GLN THR SEQRES 5 A 167 ASN PHE GLU GLY GLU ILE ILE ASP LYS ILE GLN GLU SER SEQRES 6 A 167 VAL GLY SER ASP TYR GLU GLY ILE ILE ILE ASN PRO GLY SEQRES 7 A 167 ALA PHE SER HIS THR SER ILE ALA ILE ALA ASP ALA ILE SEQRES 8 A 167 MET LEU ALA GLY LYS PRO VAL ILE GLU VAL HIS LEU THR SEQRES 9 A 167 ASN ILE GLN ALA ARG GLU GLU PHE ARG LYS ASN SER TYR SEQRES 10 A 167 THR GLY ALA ALA CYS GLY GLY VAL ILE MET GLY PHE GLY SEQRES 11 A 167 PRO LEU GLY TYR ASN MET ALA LEU MET ALA MET VAL ASN SEQRES 12 A 167 ILE LEU ALA GLU MET LYS ALA PHE GLN GLU ALA GLN LYS SEQRES 13 A 167 ASN ASN PRO ASN ASN PRO ILE ASN ASN GLN LYS SEQRES 1 B 167 MET LYS ILE LEU VAL ILE GLN GLY PRO ASN LEU ASN MET SEQRES 2 B 167 LEU GLY HIS ARG ASP PRO ARG LEU TYR GLY MET VAL THR SEQRES 3 B 167 LEU ASP GLN ILE HIS GLU ILE MET GLN THR PHE VAL LYS SEQRES 4 B 167 GLN GLY ASN LEU ASP VAL GLU LEU GLU PHE PHE GLN THR SEQRES 5 B 167 ASN PHE GLU GLY GLU ILE ILE ASP LYS ILE GLN GLU SER SEQRES 6 B 167 VAL GLY SER ASP TYR GLU GLY ILE ILE ILE ASN PRO GLY SEQRES 7 B 167 ALA PHE SER HIS THR SER ILE ALA ILE ALA ASP ALA ILE SEQRES 8 B 167 MET LEU ALA GLY LYS PRO VAL ILE GLU VAL HIS LEU THR SEQRES 9 B 167 ASN ILE GLN ALA ARG GLU GLU PHE ARG LYS ASN SER TYR SEQRES 10 B 167 THR GLY ALA ALA CYS GLY GLY VAL ILE MET GLY PHE GLY SEQRES 11 B 167 PRO LEU GLY TYR ASN MET ALA LEU MET ALA MET VAL ASN SEQRES 12 B 167 ILE LEU ALA GLU MET LYS ALA PHE GLN GLU ALA GLN LYS SEQRES 13 B 167 ASN ASN PRO ASN ASN PRO ILE ASN ASN GLN LYS SEQRES 1 C 167 MET LYS ILE LEU VAL ILE GLN GLY PRO ASN LEU ASN MET SEQRES 2 C 167 LEU GLY HIS ARG ASP PRO ARG LEU TYR GLY MET VAL THR SEQRES 3 C 167 LEU ASP GLN ILE HIS GLU ILE MET GLN THR PHE VAL LYS SEQRES 4 C 167 GLN GLY ASN LEU ASP VAL GLU LEU GLU PHE PHE GLN THR SEQRES 5 C 167 ASN PHE GLU GLY GLU ILE ILE ASP LYS ILE GLN GLU SER SEQRES 6 C 167 VAL GLY SER ASP TYR GLU GLY ILE ILE ILE ASN PRO GLY SEQRES 7 C 167 ALA PHE SER HIS THR SER ILE ALA ILE ALA ASP ALA ILE SEQRES 8 C 167 MET LEU ALA GLY LYS PRO VAL ILE GLU VAL HIS LEU THR SEQRES 9 C 167 ASN ILE GLN ALA ARG GLU GLU PHE ARG LYS ASN SER TYR SEQRES 10 C 167 THR GLY ALA ALA CYS GLY GLY VAL ILE MET GLY PHE GLY SEQRES 11 C 167 PRO LEU GLY TYR ASN MET ALA LEU MET ALA MET VAL ASN SEQRES 12 C 167 ILE LEU ALA GLU MET LYS ALA PHE GLN GLU ALA GLN LYS SEQRES 13 C 167 ASN ASN PRO ASN ASN PRO ILE ASN ASN GLN LYS HET 2HN A 200 25 HET PO4 A1159 5 HET 2HN B 200 25 HET 2HN C 200 25 HETNAM 2HN (1R,2S,4S,5R)-2-(2,3,4,5,6-PENTAFLUOROPHENYL)METHYL-1, HETNAM 2 2HN 4,5-TRIHYDROXY-3-OXOCYCLOHEXANE-1-CARBOXYLIC ACID HETNAM PO4 PHOSPHATE ION HETSYN 2HN (1R,2S,4S,5R)-2-(PERFLUOROPHENYL)METHYL-1,4,5- HETSYN 2 2HN TRIHYDROXY-3-OXOCYCLOHEXANE-1-CARBOXYLIC ACID FORMUL 4 2HN 3(C14 H11 F5 O6) FORMUL 5 PO4 O4 P 3- FORMUL 8 HOH *236(H2 O) HELIX 1 1 ASN A 10 LEU A 14 5 5 HELIX 2 2 THR A 26 GLY A 41 1 16 HELIX 3 3 PHE A 54 SER A 65 1 12 HELIX 4 4 ALA A 79 SER A 84 1 6 HELIX 5 5 SER A 84 LEU A 93 1 10 HELIX 6 6 GLU A 110 LYS A 114 5 5 HELIX 7 7 SER A 116 CYS A 122 1 7 HELIX 8 8 PRO A 131 ASN A 157 1 27 HELIX 9 9 ASN B 10 LEU B 14 5 5 HELIX 10 10 THR B 26 ASN B 42 1 17 HELIX 11 11 PHE B 54 SER B 65 1 12 HELIX 12 12 ALA B 79 SER B 84 1 6 HELIX 13 13 SER B 84 LEU B 93 1 10 HELIX 14 14 GLU B 110 LYS B 114 5 5 HELIX 15 15 SER B 116 CYS B 122 1 7 HELIX 16 16 PRO B 131 ASN B 157 1 27 HELIX 17 17 ASN C 10 LEU C 14 5 5 HELIX 18 18 THR C 26 GLY C 41 1 16 HELIX 19 19 PHE C 54 SER C 65 1 12 HELIX 20 20 PRO C 77 THR C 83 5 7 HELIX 21 21 SER C 84 LEU C 93 1 10 HELIX 22 22 GLU C 110 LYS C 114 5 5 HELIX 23 23 SER C 116 CYS C 122 1 7 HELIX 24 24 PRO C 131 ALA C 154 1 24 SHEET 1 AA 5 GLU A 46 GLN A 51 0 SHEET 2 AA 5 LYS A 2 GLN A 7 1 O ILE A 3 N GLU A 48 SHEET 3 AA 5 TYR A 70 ASN A 76 1 N GLU A 71 O LYS A 2 SHEET 4 AA 5 VAL A 98 HIS A 102 1 O ILE A 99 N ILE A 75 SHEET 5 AA 5 GLY A 124 MET A 127 1 O GLY A 124 N GLU A 100 SHEET 1 BA 5 GLU B 46 GLN B 51 0 SHEET 2 BA 5 LYS B 2 GLN B 7 1 O ILE B 3 N GLU B 48 SHEET 3 BA 5 TYR B 70 ASN B 76 1 N GLU B 71 O LYS B 2 SHEET 4 BA 5 VAL B 98 HIS B 102 1 O ILE B 99 N ILE B 75 SHEET 5 BA 5 GLY B 124 MET B 127 1 O GLY B 124 N GLU B 100 SHEET 1 CA 5 GLU C 46 GLN C 51 0 SHEET 2 CA 5 LYS C 2 GLN C 7 1 O ILE C 3 N GLU C 48 SHEET 3 CA 5 TYR C 70 ASN C 76 1 N GLU C 71 O LYS C 2 SHEET 4 CA 5 VAL C 98 HIS C 102 1 O ILE C 99 N ILE C 75 SHEET 5 CA 5 GLY C 124 MET C 127 1 O GLY C 124 N GLU C 100 SITE 1 AC1 16 ASN A 10 LEU A 11 LEU A 14 TYR A 22 SITE 2 AC1 16 ASN A 76 GLY A 78 ALA A 79 HIS A 82 SITE 3 AC1 16 HIS A 102 LEU A 103 THR A 104 ARG A 113 SITE 4 AC1 16 HOH A2005 ASP C 89 LEU C 93 HOH C2033 SITE 1 AC2 17 ASP A 89 LEU A 93 HOH A2063 HOH A2066 SITE 2 AC2 17 PRO B 9 ASN B 10 LEU B 11 LEU B 14 SITE 3 AC2 17 TYR B 22 ASN B 76 GLY B 78 ALA B 79 SITE 4 AC2 17 HIS B 82 HIS B 102 LEU B 103 THR B 104 SITE 5 AC2 17 ARG B 113 SITE 1 AC3 18 ASP B 89 LEU B 93 HOH B2045 HOH B2046 SITE 2 AC3 18 HOH B2047 PRO C 9 ASN C 10 LEU C 11 SITE 3 AC3 18 LEU C 14 TYR C 22 ASN C 76 GLY C 78 SITE 4 AC3 18 ALA C 79 HIS C 82 HIS C 102 LEU C 103 SITE 5 AC3 18 THR C 104 ARG C 113 SITE 1 AC4 5 PHE A 54 GLU A 57 PHE B 54 GLU B 57 SITE 2 AC4 5 GLU C 57 CRYST1 100.190 100.190 104.580 90.00 90.00 90.00 P 42 2 2 24 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 0.009981 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009981 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009562 0.00000