HEADER LYASE 30-APR-10 2XDA TITLE STRUCTURE OF HELICOBACTER PYLORI TYPE II DEHYDROQUINASE IN COMPLEX TITLE 2 WITH INHIBITOR COMPOUND (4R,6R,7S)-2-(2-CYCLOPROPYL)ETHYL-4,6,7- TITLE 3 TRIHYDROXY-4,5,6,7-TETRAHYDROBENZO(B)THIOPHENE-4-CARBOXYLIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3-DEHYDROQUINATE DEHYDRATASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 3-DEHYDROQUINASE; COMPND 5 EC: 4.2.1.10; COMPND 6 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: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET21A KEYWDS AROMATIC AMINO ACID BIOSYNTHESIS, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR S.PAZ,L.TIZON,J.M.OTERO,A.L.LLAMAS-SAIZ,G.C.FOX,M.J.VAN RAAIJ,H.LAMB, AUTHOR 2 A.R.HAWKINS,L.CASTEDO,C.GONZALEZ-BELLO REVDAT 5 20-DEC-23 2XDA 1 REMARK REVDAT 4 07-FEB-18 2XDA 1 JRNL REVDAT 3 31-OCT-12 2XDA 1 JRNL REVDAT 2 21-DEC-11 2XDA 1 JRNL REMARK VERSN REVDAT 1 24-NOV-10 2XDA 0 JRNL AUTH S.PAZ,L.TIZON,J.M.OTERO,A.L.LLAMAS-SAIZ,G.C.FOX, JRNL AUTH 2 M.J.VAN RAAIJ,H.LAMB,A.R.HAWKINS,A.J.LAPTHORN,L.CASTEDO, JRNL AUTH 3 C.GONZALEZ-BELLO JRNL TITL TETRAHYDROBENZOTHIOPHENE DERIVATIVES: CONFORMATIONALLY JRNL TITL 2 RESTRICTED INHIBITORS OF TYPE II DEHYDROQUINASE. JRNL REF CHEMMEDCHEM V. 6 266 2011 JRNL REFN ESSN 1860-7187 JRNL PMID 21275050 JRNL DOI 10.1002/CMDC.201000343 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 14163 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) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 770 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1993 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.2050 REMARK 3 BIN FREE R VALUE SET COUNT : 99 REMARK 3 BIN FREE R VALUE : 0.2190 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1153 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.60 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): 0.132 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.121 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.073 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.364 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1239 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 833 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1675 ; 1.374 ; 1.981 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2037 ; 0.886 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 149 ; 5.784 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 58 ;36.759 ;25.690 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 233 ;14.994 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ; 6.368 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 193 ; 0.085 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1342 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 223 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 252 ; 0.212 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 840 ; 0.178 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 594 ; 0.174 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 601 ; 0.085 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 90 ; 0.161 ; 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): 11 ; 0.184 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 18 ; 0.169 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 15 ; 0.182 ; 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): 749 ; 1.087 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 309 ; 0.243 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1217 ; 1.934 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 490 ; 2.239 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 455 ; 3.608 ; 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 WERE REFINED INDIVIDUALLY. REMARK 4 REMARK 4 2XDA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-APR-10. REMARK 100 THE DEPOSITION ID IS D_1290043780. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-DEC-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : SINGLE SILICON (111) CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14986 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 38.90 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 4.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 39.90 REMARK 200 R MERGE FOR SHELL (I) : 0.32000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.400 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 2C4V REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 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 12.5 MM (4R, 6R, 7S)- 2-(2-CYCLOPROPYL)ETHYL-4,6, REMARK 280 7-TRIHYDROXY-4,5,6, 7-TETRAHYDROBENZO[B]THIOPHENE-4-CARBOXYLIC REMARK 280 ACID 32% (W/V) POLYETHYLENEGLYCOL 4000 100 M SODIUM CITRATE PH REMARK 280 6.2 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 3 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 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 Z,X,Y REMARK 290 6555 Z,-X,-Y REMARK 290 7555 -Z,-X,Y REMARK 290 8555 -Z,X,-Y REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z,-X REMARK 290 11555 Y,-Z,-X REMARK 290 12555 -Y,-Z,X REMARK 290 13555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 14555 -Y+1/2,-X+1/2,-Z+1/2 REMARK 290 15555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 16555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 17555 X+1/2,Z+1/2,-Y+1/2 REMARK 290 18555 -X+1/2,Z+1/2,Y+1/2 REMARK 290 19555 -X+1/2,-Z+1/2,-Y+1/2 REMARK 290 20555 X+1/2,-Z+1/2,Y+1/2 REMARK 290 21555 Z+1/2,Y+1/2,-X+1/2 REMARK 290 22555 Z+1/2,-Y+1/2,X+1/2 REMARK 290 23555 -Z+1/2,Y+1/2,X+1/2 REMARK 290 24555 -Z+1/2,-Y+1/2,-X+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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 13 0.000000 1.000000 0.000000 49.82000 REMARK 290 SMTRY2 13 1.000000 0.000000 0.000000 49.82000 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 49.82000 REMARK 290 SMTRY1 14 0.000000 -1.000000 0.000000 49.82000 REMARK 290 SMTRY2 14 -1.000000 0.000000 0.000000 49.82000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 49.82000 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 49.82000 REMARK 290 SMTRY2 15 -1.000000 0.000000 0.000000 49.82000 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 49.82000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 49.82000 REMARK 290 SMTRY2 16 1.000000 0.000000 0.000000 49.82000 REMARK 290 SMTRY3 16 0.000000 0.000000 1.000000 49.82000 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 49.82000 REMARK 290 SMTRY2 17 0.000000 0.000000 1.000000 49.82000 REMARK 290 SMTRY3 17 0.000000 -1.000000 0.000000 49.82000 REMARK 290 SMTRY1 18 -1.000000 0.000000 0.000000 49.82000 REMARK 290 SMTRY2 18 0.000000 0.000000 1.000000 49.82000 REMARK 290 SMTRY3 18 0.000000 1.000000 0.000000 49.82000 REMARK 290 SMTRY1 19 -1.000000 0.000000 0.000000 49.82000 REMARK 290 SMTRY2 19 0.000000 0.000000 -1.000000 49.82000 REMARK 290 SMTRY3 19 0.000000 -1.000000 0.000000 49.82000 REMARK 290 SMTRY1 20 1.000000 0.000000 0.000000 49.82000 REMARK 290 SMTRY2 20 0.000000 0.000000 -1.000000 49.82000 REMARK 290 SMTRY3 20 0.000000 1.000000 0.000000 49.82000 REMARK 290 SMTRY1 21 0.000000 0.000000 1.000000 49.82000 REMARK 290 SMTRY2 21 0.000000 1.000000 0.000000 49.82000 REMARK 290 SMTRY3 21 -1.000000 0.000000 0.000000 49.82000 REMARK 290 SMTRY1 22 0.000000 0.000000 1.000000 49.82000 REMARK 290 SMTRY2 22 0.000000 -1.000000 0.000000 49.82000 REMARK 290 SMTRY3 22 1.000000 0.000000 0.000000 49.82000 REMARK 290 SMTRY1 23 0.000000 0.000000 -1.000000 49.82000 REMARK 290 SMTRY2 23 0.000000 1.000000 0.000000 49.82000 REMARK 290 SMTRY3 23 1.000000 0.000000 0.000000 49.82000 REMARK 290 SMTRY1 24 0.000000 0.000000 -1.000000 49.82000 REMARK 290 SMTRY2 24 0.000000 -1.000000 0.000000 49.82000 REMARK 290 SMTRY3 24 -1.000000 0.000000 0.000000 49.82000 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: 28320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 65160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -179.8 KCAL/MOL 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 350 BIOMT1 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT3 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT2 3 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 -1.000000 0.000000 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 350 BIOMT1 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT2 5 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 6 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 7 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 7 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT3 7 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT1 8 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 9 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 9 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT3 9 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT1 10 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT2 10 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 10 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT1 11 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 11 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT1 12 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT2 12 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 12 0.000000 -1.000000 0.000000 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 A2016 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2026 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2027 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2041 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2081 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 PHE A 151 REMARK 465 GLN A 152 REMARK 465 GLU A 153 REMARK 465 ALA A 154 REMARK 465 GLN A 155 REMARK 465 LYS A 156 REMARK 465 ASN A 157 REMARK 465 ASN A 158 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 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 -11.76 76.24 REMARK 500 VAL A 66 86.83 -64.57 REMARK 500 ARG A 109 -146.90 -121.43 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 A2012 DISTANCE = 6.06 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE JPS A 1151 REMARK 900 REMARK 900 RELATED ENTRIES 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: 2C4V RELATED DB: PDB REMARK 900 H. PYLORI TYPE II DHQASE IN COMPLEX WITH CITRATE REMARK 900 RELATED ID: 1J2Y RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE TYPE II 3- DEHYDROQUINASE 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: 2C4W RELATED DB: PDB REMARK 900 TYPE II DEHYDROQUINASE FROM H. PYLORI IN COMPLEX WITH AH9095 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 DBREF 2XDA A 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 HET JPS A1151 20 HETNAM JPS (4R,6R,7S)-2-(2-CYCLOPROPYLETHYL)-4,6,7-TRIHYDROXY-4,5, HETNAM 2 JPS 6,7-TETRAHYDRO-1-BENZOTHIOPHENE-4-CARBOXYLIC ACID FORMUL 2 JPS C14 H18 O5 S FORMUL 3 HOH *110(H2 O) HELIX 1 1 ASN A 10 LEU A 14 5 5 HELIX 2 2 ASP A 18 GLY A 23 1 6 HELIX 3 3 THR A 26 GLY A 41 1 16 HELIX 4 4 PHE A 54 SER A 65 1 12 HELIX 5 5 ALA A 79 SER A 84 1 6 HELIX 6 6 SER A 84 GLY A 95 1 12 HELIX 7 7 GLU A 110 LYS A 114 5 5 HELIX 8 8 SER A 116 CYS A 122 1 7 HELIX 9 9 PRO A 131 ALA A 150 1 20 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 SITE 1 AC1 14 ASN A 10 MET A 13 ARG A 17 TYR A 22 SITE 2 AC1 14 ASN A 76 GLY A 78 ALA A 79 HIS A 82 SITE 3 AC1 14 ASP A 89 LEU A 93 HIS A 102 LEU A 103 SITE 4 AC1 14 THR A 104 ARG A 113 CRYST1 99.640 99.640 99.640 90.00 90.00 90.00 P 42 3 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 0.010036 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010036 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010036 0.00000