HEADER CHAPERONE 12-JUN-11 3SF5 TITLE CRYSTAL STRUCTURE OF HELICOBACTER PYLORI UREASE ACCESSORY PROTEIN TITLE 2 UREF/H COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: UREASE ACCESSORY PROTEIN UREF; COMPND 3 CHAIN: A, C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: UREASE ACCESSORY PROTEIN UREH; COMPND 7 CHAIN: B, D; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI; SOURCE 3 ORGANISM_TAXID: 210; SOURCE 4 GENE: UREF; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI; SOURCE 9 ORGANISM_TAXID: 210; SOURCE 10 GENE: UREH; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS UREASE ACCESSORY PROTEIN, UREF, UREH, CHAPERONE EXPDTA X-RAY DIFFRACTION AUTHOR Y.H.FONG,Y.W.CHEN,K.B.WONG REVDAT 3 01-NOV-23 3SF5 1 REMARK REVDAT 2 01-FEB-12 3SF5 1 JRNL REVDAT 1 02-NOV-11 3SF5 0 JRNL AUTH Y.H.FONG,H.C.WONG,C.P.CHUCK,Y.W.CHEN,H.SUN,K.B.WONG JRNL TITL ASSEMBLY OF PREACTIVATION COMPLEX FOR UREASE MATURATION IN JRNL TITL 2 HELICOBACTER PYLORI: CRYSTAL STRUCTURE OF UREF-UREH PROTEIN JRNL TITL 3 COMPLEX JRNL REF J.BIOL.CHEM. V. 286 43241 2011 JRNL REFN ISSN 0021-9258 JRNL PMID 22013070 JRNL DOI 10.1074/JBC.M111.296830 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.4_486) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 36383 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1820 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 35.8304 - 5.8589 1.00 2858 151 0.1856 0.1992 REMARK 3 2 5.8589 - 4.6536 1.00 2758 145 0.1820 0.2187 REMARK 3 3 4.6536 - 4.0663 1.00 2717 143 0.1436 0.1826 REMARK 3 4 4.0663 - 3.6949 1.00 2667 141 0.1606 0.2040 REMARK 3 5 3.6949 - 3.4303 1.00 2682 141 0.1637 0.1980 REMARK 3 6 3.4303 - 3.2282 1.00 2647 139 0.1802 0.2218 REMARK 3 7 3.2282 - 3.0666 1.00 2670 141 0.1772 0.2270 REMARK 3 8 3.0666 - 2.9332 1.00 2651 139 0.1683 0.2201 REMARK 3 9 2.9332 - 2.8203 1.00 2617 138 0.1782 0.2162 REMARK 3 10 2.8203 - 2.7230 1.00 2653 140 0.1757 0.2548 REMARK 3 11 2.7230 - 2.6379 0.99 2635 138 0.1866 0.2653 REMARK 3 12 2.6379 - 2.5625 0.99 2628 139 0.2016 0.2822 REMARK 3 13 2.5625 - 2.4951 0.90 2380 125 0.2062 0.2916 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.95 REMARK 3 K_SOL : 0.37 REMARK 3 B_SOL : 30.07 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.830 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.96 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.73 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.20370 REMARK 3 B22 (A**2) : -1.32730 REMARK 3 B33 (A**2) : 2.53100 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.003 7975 REMARK 3 ANGLE : 0.692 10747 REMARK 3 CHIRALITY : 0.049 1225 REMARK 3 PLANARITY : 0.002 1373 REMARK 3 DIHEDRAL : 13.316 3004 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 2 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN A AND (RESSEQ 29:254 ) REMARK 3 SELECTION : CHAIN C AND (RESSEQ 29:254 ) REMARK 3 ATOM PAIRS NUMBER : 1799 REMARK 3 RMSD : 0.312 REMARK 3 NCS GROUP : 2 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN B AND (RESSEQ 6:260 ) REMARK 3 SELECTION : CHAIN D AND (RESSEQ 6:260 ) REMARK 3 ATOM PAIRS NUMBER : 2005 REMARK 3 RMSD : 0.327 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3SF5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-JUL-11. REMARK 100 THE DEPOSITION ID IS D_1000066126. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-APR-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NI MIRROR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36388 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.495 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.65 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 3O1Q REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% PEG 4000, 0.15M AMMONIUM SULFATE, REMARK 280 0.1M MES, PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 35.32650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 102.74950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.36600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 102.74950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.32650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.36600 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 13120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 38140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -101.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 1 REMARK 465 ASP A 2 REMARK 465 LYS A 3 REMARK 465 GLY A 4 REMARK 465 LYS A 5 REMARK 465 SER A 6 REMARK 465 VAL A 7 REMARK 465 LYS A 8 REMARK 465 SER A 9 REMARK 465 THR A 10 REMARK 465 GLU A 11 REMARK 465 LYS A 12 REMARK 465 SER A 13 REMARK 465 VAL A 14 REMARK 465 GLY A 15 REMARK 465 MET A 16 REMARK 465 PRO A 17 REMARK 465 PRO A 18 REMARK 465 LYS A 19 REMARK 465 THR A 20 REMARK 465 PRO A 21 REMARK 465 LYS A 22 REMARK 465 THR A 23 REMARK 465 ASP A 24 REMARK 465 ASN A 25 REMARK 465 MET B 1 REMARK 465 ASN B 2 REMARK 465 THR B 3 REMARK 465 TYR B 4 REMARK 465 MET C 1 REMARK 465 ASP C 2 REMARK 465 LYS C 3 REMARK 465 GLY C 4 REMARK 465 LYS C 5 REMARK 465 SER C 6 REMARK 465 VAL C 7 REMARK 465 LYS C 8 REMARK 465 SER C 9 REMARK 465 THR C 10 REMARK 465 GLU C 11 REMARK 465 LYS C 12 REMARK 465 SER C 13 REMARK 465 VAL C 14 REMARK 465 GLY C 15 REMARK 465 MET C 16 REMARK 465 PRO C 17 REMARK 465 PRO C 18 REMARK 465 LYS C 19 REMARK 465 THR C 20 REMARK 465 PRO C 21 REMARK 465 LYS C 22 REMARK 465 THR C 23 REMARK 465 ASP C 24 REMARK 465 MET D 1 REMARK 465 THR D 262 REMARK 465 GLN D 263 REMARK 465 LYS D 264 REMARK 465 VAL D 265 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 SER A 79 -92.32 -119.03 REMARK 500 VAL A 235 -77.85 -108.30 REMARK 500 LYS B 34 124.08 -171.90 REMARK 500 PRO B 41 -75.65 -51.89 REMARK 500 ASN B 72 -7.16 71.18 REMARK 500 GLU B 89 -122.64 56.33 REMARK 500 ASN B 156 -72.34 -73.11 REMARK 500 MET B 190 -110.04 -105.10 REMARK 500 SER B 232 32.45 72.82 REMARK 500 ASN C 26 40.28 80.92 REMARK 500 SER C 79 -91.74 -120.64 REMARK 500 ASP C 100 76.62 -103.34 REMARK 500 VAL C 235 -81.10 -111.48 REMARK 500 PRO D 41 -71.99 -57.95 REMARK 500 ASN D 72 -5.03 68.89 REMARK 500 GLU D 89 -121.72 55.09 REMARK 500 ASN D 104 17.17 56.24 REMARK 500 MET D 190 -114.68 -108.12 REMARK 500 SER D 232 30.43 71.56 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 PEG A 255 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 256 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 257 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 258 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 259 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 266 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 267 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG B 268 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG B 269 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG C 255 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG C 256 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 257 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 258 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 D 266 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 D 267 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG D 268 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3O1Q RELATED DB: PDB REMARK 900 NATIVE CRYSTAL STRUCTURE OF HELICOBACTER PYLORI UREF REMARK 900 RELATED ID: 2WGL RELATED DB: PDB REMARK 900 SELENOMETHIONINE CRYSTAL STRUCTURE OF HELICOBACTER PYLORI UREF DBREF 3SF5 A 1 254 UNP Q09065 UREF_HELPY 1 254 DBREF 3SF5 B 1 265 UNP Q09067 UREH_HELPY 1 265 DBREF 3SF5 C 1 254 UNP Q09065 UREF_HELPY 1 254 DBREF 3SF5 D 1 265 UNP Q09067 UREH_HELPY 1 265 SEQRES 1 A 254 MET ASP LYS GLY LYS SER VAL LYS SER THR GLU LYS SER SEQRES 2 A 254 VAL GLY MET PRO PRO LYS THR PRO LYS THR ASP ASN ASN SEQRES 3 A 254 ALA HIS VAL ASP ASN GLU PHE LEU ILE LEU GLN VAL ASN SEQRES 4 A 254 ASP ALA VAL PHE PRO ILE GLY SER TYR THR HIS SER PHE SEQRES 5 A 254 GLY LEU GLU THR TYR ILE GLN GLN LYS LYS VAL THR ASN SEQRES 6 A 254 LYS GLU SER ALA LEU GLU TYR LEU LYS ALA ASN LEU SER SEQRES 7 A 254 SER GLN PHE LEU TYR THR GLU MET LEU SER LEU LYS LEU SEQRES 8 A 254 THR TYR GLU SER ALA LEU GLN GLN ASP LEU LYS LYS ILE SEQRES 9 A 254 LEU GLY VAL GLU GLU VAL ILE MET LEU SER THR SER PRO SEQRES 10 A 254 MET GLU LEU ARG LEU ALA ASN GLN LYS LEU GLY ASN ARG SEQRES 11 A 254 PHE ILE LYS THR LEU GLN ALA MET ASN GLU LEU ASP MET SEQRES 12 A 254 GLY GLU PHE PHE ASN ALA TYR ALA GLN LYS THR LYS ASP SEQRES 13 A 254 PRO THR HIS ALA THR SER TYR GLY VAL PHE ALA ALA SER SEQRES 14 A 254 LEU GLY ILE GLU LEU LYS LYS ALA LEU ARG HIS TYR LEU SEQRES 15 A 254 TYR ALA GLN THR SER ASN MET VAL ILE ASN CYS VAL LYS SEQRES 16 A 254 SER VAL PRO LEU SER GLN ASN ASP GLY GLN LYS ILE LEU SEQRES 17 A 254 LEU SER LEU GLN SER PRO PHE ASN GLN LEU ILE GLU LYS SEQRES 18 A 254 THR LEU GLU LEU ASP GLU SER HIS LEU CYS THR ALA SER SEQRES 19 A 254 VAL GLN ASN ASP ILE LYS ALA MET GLN HIS GLU SER LEU SEQRES 20 A 254 TYR SER ARG LEU TYR MET SER SEQRES 1 B 265 MET ASN THR TYR ALA GLN GLU SER LYS LEU ARG LEU LYS SEQRES 2 B 265 THR LYS ILE GLY ALA ASP GLY ARG CYS VAL ILE GLU ASP SEQRES 3 B 265 ASN PHE PHE THR PRO PRO PHE LYS LEU MET ALA PRO PHE SEQRES 4 B 265 TYR PRO LYS ASP ASP LEU ALA GLU ILE MET LEU LEU ALA SEQRES 5 B 265 VAL SER PRO GLY MET MET ARG GLY ASP ALA GLN ASP VAL SEQRES 6 B 265 GLN LEU ASN ILE GLY PRO ASN CYS LYS LEU ARG ILE THR SEQRES 7 B 265 SER GLN SER PHE GLU LYS ILE HIS ASN THR GLU ASP GLY SEQRES 8 B 265 PHE ALA SER ARG ASP MET HIS ILE VAL VAL GLY GLU ASN SEQRES 9 B 265 ALA PHE LEU ASP PHE ALA PRO PHE PRO LEU ILE PRO PHE SEQRES 10 B 265 GLU ASN ALA HIS PHE LYS GLY ASN THR THR ILE SER LEU SEQRES 11 B 265 ARG SER SER SER GLN LEU LEU TYR SER GLU ILE ILE VAL SEQRES 12 B 265 ALA GLY ARG VAL ALA ARG ASN GLU LEU PHE LYS PHE ASN SEQRES 13 B 265 ARG LEU HIS THR LYS ILE SER ILE LEU GLN ASP GLU LYS SEQRES 14 B 265 PRO ILE TYR TYR ASP ASN THR ILE LEU ASP PRO LYS THR SEQRES 15 B 265 THR ASP LEU ASN ASN MET CYS MET PHE ASP GLY TYR THR SEQRES 16 B 265 HIS TYR LEU ASN LEU VAL LEU VAL ASN CYS PRO ILE GLU SEQRES 17 B 265 LEU SER GLY VAL ARG GLU CYS ILE GLU GLU SER GLU GLY SEQRES 18 B 265 VAL ASP GLY ALA VAL SER GLU THR ALA SER SER HIS LEU SEQRES 19 B 265 CYS VAL LYS ALA LEU ALA LYS GLY SER GLU PRO LEU LEU SEQRES 20 B 265 HIS LEU ARG GLU LYS ILE ALA ARG LEU VAL THR GLN THR SEQRES 21 B 265 THR THR GLN LYS VAL SEQRES 1 C 254 MET ASP LYS GLY LYS SER VAL LYS SER THR GLU LYS SER SEQRES 2 C 254 VAL GLY MET PRO PRO LYS THR PRO LYS THR ASP ASN ASN SEQRES 3 C 254 ALA HIS VAL ASP ASN GLU PHE LEU ILE LEU GLN VAL ASN SEQRES 4 C 254 ASP ALA VAL PHE PRO ILE GLY SER TYR THR HIS SER PHE SEQRES 5 C 254 GLY LEU GLU THR TYR ILE GLN GLN LYS LYS VAL THR ASN SEQRES 6 C 254 LYS GLU SER ALA LEU GLU TYR LEU LYS ALA ASN LEU SER SEQRES 7 C 254 SER GLN PHE LEU TYR THR GLU MET LEU SER LEU LYS LEU SEQRES 8 C 254 THR TYR GLU SER ALA LEU GLN GLN ASP LEU LYS LYS ILE SEQRES 9 C 254 LEU GLY VAL GLU GLU VAL ILE MET LEU SER THR SER PRO SEQRES 10 C 254 MET GLU LEU ARG LEU ALA ASN GLN LYS LEU GLY ASN ARG SEQRES 11 C 254 PHE ILE LYS THR LEU GLN ALA MET ASN GLU LEU ASP MET SEQRES 12 C 254 GLY GLU PHE PHE ASN ALA TYR ALA GLN LYS THR LYS ASP SEQRES 13 C 254 PRO THR HIS ALA THR SER TYR GLY VAL PHE ALA ALA SER SEQRES 14 C 254 LEU GLY ILE GLU LEU LYS LYS ALA LEU ARG HIS TYR LEU SEQRES 15 C 254 TYR ALA GLN THR SER ASN MET VAL ILE ASN CYS VAL LYS SEQRES 16 C 254 SER VAL PRO LEU SER GLN ASN ASP GLY GLN LYS ILE LEU SEQRES 17 C 254 LEU SER LEU GLN SER PRO PHE ASN GLN LEU ILE GLU LYS SEQRES 18 C 254 THR LEU GLU LEU ASP GLU SER HIS LEU CYS THR ALA SER SEQRES 19 C 254 VAL GLN ASN ASP ILE LYS ALA MET GLN HIS GLU SER LEU SEQRES 20 C 254 TYR SER ARG LEU TYR MET SER SEQRES 1 D 265 MET ASN THR TYR ALA GLN GLU SER LYS LEU ARG LEU LYS SEQRES 2 D 265 THR LYS ILE GLY ALA ASP GLY ARG CYS VAL ILE GLU ASP SEQRES 3 D 265 ASN PHE PHE THR PRO PRO PHE LYS LEU MET ALA PRO PHE SEQRES 4 D 265 TYR PRO LYS ASP ASP LEU ALA GLU ILE MET LEU LEU ALA SEQRES 5 D 265 VAL SER PRO GLY MET MET ARG GLY ASP ALA GLN ASP VAL SEQRES 6 D 265 GLN LEU ASN ILE GLY PRO ASN CYS LYS LEU ARG ILE THR SEQRES 7 D 265 SER GLN SER PHE GLU LYS ILE HIS ASN THR GLU ASP GLY SEQRES 8 D 265 PHE ALA SER ARG ASP MET HIS ILE VAL VAL GLY GLU ASN SEQRES 9 D 265 ALA PHE LEU ASP PHE ALA PRO PHE PRO LEU ILE PRO PHE SEQRES 10 D 265 GLU ASN ALA HIS PHE LYS GLY ASN THR THR ILE SER LEU SEQRES 11 D 265 ARG SER SER SER GLN LEU LEU TYR SER GLU ILE ILE VAL SEQRES 12 D 265 ALA GLY ARG VAL ALA ARG ASN GLU LEU PHE LYS PHE ASN SEQRES 13 D 265 ARG LEU HIS THR LYS ILE SER ILE LEU GLN ASP GLU LYS SEQRES 14 D 265 PRO ILE TYR TYR ASP ASN THR ILE LEU ASP PRO LYS THR SEQRES 15 D 265 THR ASP LEU ASN ASN MET CYS MET PHE ASP GLY TYR THR SEQRES 16 D 265 HIS TYR LEU ASN LEU VAL LEU VAL ASN CYS PRO ILE GLU SEQRES 17 D 265 LEU SER GLY VAL ARG GLU CYS ILE GLU GLU SER GLU GLY SEQRES 18 D 265 VAL ASP GLY ALA VAL SER GLU THR ALA SER SER HIS LEU SEQRES 19 D 265 CYS VAL LYS ALA LEU ALA LYS GLY SER GLU PRO LEU LEU SEQRES 20 D 265 HIS LEU ARG GLU LYS ILE ALA ARG LEU VAL THR GLN THR SEQRES 21 D 265 THR THR GLN LYS VAL HET PEG A 255 7 HET PEG A 256 7 HET PEG A 257 7 HET PEG A 258 7 HET GOL A 259 6 HET SO4 B 266 5 HET SO4 B 267 5 HET PEG B 268 7 HET PEG B 269 7 HET PEG C 255 7 HET PEG C 256 7 HET GOL C 257 6 HET SO4 C 258 5 HET SO4 D 266 5 HET SO4 D 267 5 HET PEG D 268 7 HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 PEG 9(C4 H10 O3) FORMUL 9 GOL 2(C3 H8 O3) FORMUL 10 SO4 5(O4 S 2-) FORMUL 21 HOH *207(H2 O) HELIX 1 1 ASP A 30 ASP A 40 1 11 HELIX 2 2 GLY A 46 HIS A 50 5 5 HELIX 3 3 GLY A 53 GLN A 60 1 8 HELIX 4 4 ASN A 65 SER A 78 1 14 HELIX 5 5 SER A 79 THR A 84 1 6 HELIX 6 6 THR A 84 GLN A 98 1 15 HELIX 7 7 ASP A 100 THR A 115 1 16 HELIX 8 8 PRO A 117 MET A 138 1 22 HELIX 9 9 GLY A 144 THR A 154 1 11 HELIX 10 10 THR A 158 GLY A 171 1 14 HELIX 11 11 GLU A 173 VAL A 197 1 25 HELIX 12 12 SER A 200 LEU A 211 1 12 HELIX 13 13 LEU A 211 LEU A 225 1 15 HELIX 14 14 ASP A 226 LEU A 230 5 5 HELIX 15 15 VAL A 235 HIS A 244 1 10 HELIX 16 16 GLU A 245 LEU A 247 5 3 HELIX 17 17 ARG B 146 ASN B 150 5 5 HELIX 18 18 GLU B 208 GLU B 218 1 11 HELIX 19 19 GLY B 242 GLN B 259 1 18 HELIX 20 20 ASP C 30 ASP C 40 1 11 HELIX 21 21 GLY C 46 HIS C 50 5 5 HELIX 22 22 GLY C 53 GLN C 60 1 8 HELIX 23 23 ASN C 65 SER C 78 1 14 HELIX 24 24 SER C 79 THR C 84 1 6 HELIX 25 25 THR C 84 GLN C 98 1 15 HELIX 26 26 ASP C 100 THR C 115 1 16 HELIX 27 27 PRO C 117 MET C 138 1 22 HELIX 28 28 GLY C 144 THR C 154 1 11 HELIX 29 29 THR C 158 GLY C 171 1 14 HELIX 30 30 GLU C 173 VAL C 197 1 25 HELIX 31 31 SER C 200 LEU C 211 1 12 HELIX 32 32 LEU C 211 LEU C 225 1 15 HELIX 33 33 ASP C 226 LEU C 230 5 5 HELIX 34 34 VAL C 235 HIS C 244 1 10 HELIX 35 35 GLU C 245 LEU C 247 5 3 HELIX 36 36 ARG D 146 ASN D 150 5 5 HELIX 37 37 GLU D 208 GLU D 218 1 11 HELIX 38 38 GLY D 242 GLN D 259 1 18 SHEET 1 A 7 CYS B 22 PHE B 29 0 SHEET 2 A 7 GLU B 7 ILE B 16 -1 N ARG B 11 O PHE B 28 SHEET 3 A 7 ALA B 62 ILE B 69 1 O ASN B 68 N LEU B 12 SHEET 4 A 7 ALA B 93 VAL B 101 1 O ASP B 96 N VAL B 65 SHEET 5 A 7 HIS B 121 LEU B 130 1 O SER B 129 N ILE B 99 SHEET 6 A 7 ARG B 157 GLN B 166 1 O LEU B 165 N ILE B 128 SHEET 7 A 7 LYS B 169 LEU B 178 -1 O LYS B 169 N GLN B 166 SHEET 1 B 8 PHE B 33 LEU B 35 0 SHEET 2 B 8 ALA B 46 ALA B 52 -1 O LEU B 51 N LYS B 34 SHEET 3 B 8 LYS B 74 THR B 78 1 O LYS B 74 N ALA B 46 SHEET 4 B 8 PHE B 106 PHE B 109 1 O PHE B 106 N LEU B 75 SHEET 5 B 8 GLN B 135 VAL B 143 1 O LEU B 137 N LEU B 107 SHEET 6 B 8 HIS B 196 VAL B 203 -1 O VAL B 201 N TYR B 138 SHEET 7 B 8 LEU B 234 ALA B 240 -1 O VAL B 236 N LEU B 200 SHEET 8 B 8 VAL B 222 GLU B 228 -1 N ASP B 223 O LEU B 239 SHEET 1 C 2 GLU B 83 ILE B 85 0 SHEET 2 C 2 LEU B 114 PRO B 116 1 O ILE B 115 N GLU B 83 SHEET 1 D 7 CYS D 22 PHE D 29 0 SHEET 2 D 7 GLU D 7 ILE D 16 -1 N LYS D 13 O ASP D 26 SHEET 3 D 7 ALA D 62 ILE D 69 1 O GLN D 66 N LEU D 10 SHEET 4 D 7 ALA D 93 VAL D 101 1 O ASP D 96 N GLN D 63 SHEET 5 D 7 HIS D 121 LEU D 130 1 O SER D 129 N ILE D 99 SHEET 6 D 7 ARG D 157 GLN D 166 1 O LEU D 165 N LEU D 130 SHEET 7 D 7 LYS D 169 LEU D 178 -1 O LYS D 169 N GLN D 166 SHEET 1 E 8 PHE D 33 LEU D 35 0 SHEET 2 E 8 ALA D 46 ALA D 52 -1 O LEU D 51 N LYS D 34 SHEET 3 E 8 LYS D 74 THR D 78 1 O THR D 78 N LEU D 50 SHEET 4 E 8 PHE D 106 PHE D 109 1 O ASP D 108 N ILE D 77 SHEET 5 E 8 GLN D 135 VAL D 143 1 O LEU D 137 N LEU D 107 SHEET 6 E 8 HIS D 196 VAL D 203 -1 O VAL D 201 N TYR D 138 SHEET 7 E 8 LEU D 234 ALA D 240 -1 O VAL D 236 N LEU D 200 SHEET 8 E 8 ASP D 223 GLU D 228 -1 N ASP D 223 O LEU D 239 SHEET 1 F 2 GLU D 83 ILE D 85 0 SHEET 2 F 2 LEU D 114 PRO D 116 1 O ILE D 115 N GLU D 83 CISPEP 1 VAL A 197 PRO A 198 0 -1.94 CISPEP 2 PRO B 31 PRO B 32 0 4.15 CISPEP 3 VAL C 197 PRO C 198 0 -2.32 CISPEP 4 PRO D 31 PRO D 32 0 0.57 SITE 1 AC1 3 LYS A 195 LEU A 251 TYR A 252 SITE 1 AC2 3 LEU A 230 HOH A 291 LYS B 161 SITE 1 AC3 4 SER A 200 GLN A 201 ASN A 202 ASP A 203 SITE 1 AC4 7 VAL A 38 ASN A 39 SER A 47 HIS A 159 SITE 2 AC4 7 TYR A 181 GLN A 185 ASN A 188 SITE 1 AC5 7 GLN A 80 THR A 84 SER A 114 THR A 115 SITE 2 AC5 7 ALA A 233 SER A 234 ASP A 238 SITE 1 AC6 5 HIS B 86 ASN B 87 PHE B 117 HOH B 291 SITE 2 AC6 5 HOH B 304 SITE 1 AC7 4 HIS B 121 LYS B 123 ARG B 157 HIS B 159 SITE 1 AC8 4 HIS B 196 GLY B 242 SER B 243 GLU B 244 SITE 1 AC9 3 ASN B 186 ASP B 192 HOH B 286 SITE 1 BC1 5 ALA A 137 ASN A 139 SER C 200 ASN C 202 SITE 2 BC1 5 LYS C 206 SITE 1 BC2 2 TYR C 48 LEU C 251 SITE 1 BC3 9 GLN C 80 THR C 84 SER C 114 THR C 115 SITE 2 BC3 9 CYS C 231 ALA C 233 SER C 234 ASP C 238 SITE 3 BC3 9 HOH C 267 SITE 1 BC4 7 LYS A 176 ARG A 179 HIS A 180 LYS C 176 SITE 2 BC4 7 ARG C 179 HIS C 180 HOH C 321 SITE 1 BC5 4 HIS D 121 LYS D 123 ARG D 157 HIS D 159 SITE 1 BC6 2 HIS D 86 ASN D 87 SITE 1 BC7 4 HIS D 196 GLY D 242 SER D 243 GLU D 244 CRYST1 70.653 70.732 205.499 90.00 90.00 90.00 P 21 21 21 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 0.014154 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014138 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004866 0.00000