HEADER DNA BINDING PROTEIN 31-JUL-09 2WP0 TITLE CRYSTAL STRUCTURE OF A HOBA-DNAA (DOMAIN I-II) COMPLEX FROM TITLE 2 HELICOBACTER PYLORI. COMPND MOL_ID: 1; COMPND 2 MOLECULE: HOBA; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: HOBA PROTEIN (HP 1230); COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: CHROMOSOMAL REPLICATION INITIATOR PROTEIN DNAA; COMPND 8 CHAIN: C, D; COMPND 9 FRAGMENT: DOMAIN I-II, RESIDUES 1-120; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: N-TERMINAL FRAGMENT OF DNAA 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_VECTOR: PRSF; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI; SOURCE 10 ORGANISM_TAXID: 210; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 13 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 14 EXPRESSION_SYSTEM_VECTOR: PET151 KEYWDS DNA BINDING PROTEIN, NUCLEOTIDE-BINDING, DNA REPLICATION INITIATION, KEYWDS 2 DIAA, HOBA, DNAA, ATP-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR G.NATRAJAN,M.-F.NOIROT-GROS,A.ZAWILAK-PAWLIK,U.KAPP,L.TERRADOT REVDAT 5 20-DEC-23 2WP0 1 LINK REVDAT 4 12-JUL-17 2WP0 1 REVDAT 3 29-DEC-09 2WP0 1 JRNL REVDAT 2 08-DEC-09 2WP0 1 JRNL REVDAT 1 17-NOV-09 2WP0 0 JRNL AUTH G.NATRAJAN,M.F.NOIROT-GROS,A.ZAWILAK-PAWLIK,U.KAPP, JRNL AUTH 2 L.TERRADOT JRNL TITL THE STRUCTURE OF A DNAA/HOBA COMPLEX FROM HELICOBACTER JRNL TITL 2 PYLORI PROVIDES INSIGHT INTO REGULATION OF DNA REPLICATION JRNL TITL 3 IN BACTERIA. JRNL REF PROC.NATL.ACAD.SCI.USA V. 106 21115 2009 JRNL REFN ISSN 0027-8424 JRNL PMID 19940251 JRNL DOI 10.1073/PNAS.0908966106 REMARK 2 REMARK 2 RESOLUTION. 2.67 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 2.67 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.4 REMARK 3 NUMBER OF REFLECTIONS : 17357 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.170 REMARK 3 FREE R VALUE TEST SET COUNT : 897 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 50.7648 - 4.8506 0.83 2605 133 0.1839 0.1992 REMARK 3 2 4.8506 - 3.8504 0.90 2739 143 0.1734 0.2134 REMARK 3 3 3.8504 - 3.3638 0.92 2813 146 0.2169 0.2319 REMARK 3 4 3.3638 - 3.0563 0.94 2816 170 0.2472 0.3095 REMARK 3 5 3.0563 - 2.8373 0.94 2820 155 0.2918 0.3377 REMARK 3 6 2.8373 - 2.6700 0.90 2667 150 0.3135 0.3843 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.38 REMARK 3 B_SOL : 60.00 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.410 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.950 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.93130 REMARK 3 B22 (A**2) : -1.83360 REMARK 3 B33 (A**2) : 9.80060 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.90370 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 : 0.011 4451 REMARK 3 ANGLE : 1.506 6019 REMARK 3 CHIRALITY : 0.117 675 REMARK 3 PLANARITY : 0.006 751 REMARK 3 DIHEDRAL : 21.244 1610 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 17.0163 -17.2043 10.0061 REMARK 3 T TENSOR REMARK 3 T11: 0.1875 T22: 0.1473 REMARK 3 T33: 0.2362 T12: -0.0183 REMARK 3 T13: -0.0196 T23: -0.0271 REMARK 3 L TENSOR REMARK 3 L11: 0.7171 L22: 0.2752 REMARK 3 L33: 0.9491 L12: -0.0739 REMARK 3 L13: -0.4382 L23: -0.1594 REMARK 3 S TENSOR REMARK 3 S11: 0.0647 S12: 0.0215 S13: 0.1114 REMARK 3 S21: 0.0691 S22: 0.0456 S23: -0.0217 REMARK 3 S31: -0.0619 S32: 0.0700 S33: -0.1137 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): 16.8997 -26.2902 -9.9762 REMARK 3 T TENSOR REMARK 3 T11: 0.1957 T22: 0.1410 REMARK 3 T33: 0.2419 T12: 0.0056 REMARK 3 T13: 0.0118 T23: -0.0336 REMARK 3 L TENSOR REMARK 3 L11: 0.5651 L22: 0.3110 REMARK 3 L33: 0.9586 L12: -0.0596 REMARK 3 L13: 0.5318 L23: 0.0330 REMARK 3 S TENSOR REMARK 3 S11: 0.0657 S12: 0.0093 S13: -0.0381 REMARK 3 S21: -0.0737 S22: 0.0487 S23: -0.0568 REMARK 3 S31: 0.0525 S32: 0.0627 S33: -0.1105 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN C REMARK 3 ORIGIN FOR THE GROUP (A): 12.8329 -43.9992 32.8747 REMARK 3 T TENSOR REMARK 3 T11: 0.2520 T22: 0.2706 REMARK 3 T33: 0.3794 T12: -0.1020 REMARK 3 T13: -0.1165 T23: 0.1127 REMARK 3 L TENSOR REMARK 3 L11: 0.3952 L22: 0.7753 REMARK 3 L33: 1.6672 L12: 0.5421 REMARK 3 L13: 0.2571 L23: 0.0720 REMARK 3 S TENSOR REMARK 3 S11: 0.0981 S12: -0.0228 S13: -0.4194 REMARK 3 S21: -0.0391 S22: -0.3596 S23: -0.5849 REMARK 3 S31: 0.1988 S32: -0.1915 S33: 0.0710 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN D REMARK 3 ORIGIN FOR THE GROUP (A): 12.6415 0.8027 -32.8355 REMARK 3 T TENSOR REMARK 3 T11: 0.2466 T22: 0.1799 REMARK 3 T33: 0.2485 T12: 0.0658 REMARK 3 T13: 0.0738 T23: 0.0411 REMARK 3 L TENSOR REMARK 3 L11: 0.4787 L22: 0.1633 REMARK 3 L33: 1.0388 L12: -0.2443 REMARK 3 L13: -0.2417 L23: -0.0577 REMARK 3 S TENSOR REMARK 3 S11: 0.0520 S12: -0.0783 S13: 0.2424 REMARK 3 S21: -0.0890 S22: -0.0757 S23: -0.2727 REMARK 3 S31: -0.3150 S32: -0.1912 S33: -0.0399 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 1:180 ) REMARK 3 SELECTION : CHAIN B AND (RESSEQ 1:180 ) REMARK 3 ATOM PAIRS NUMBER : 1487 REMARK 3 RMSD : 0.273 REMARK 3 NCS GROUP : 2 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN C AND (RESSEQ 10:74 OR RESSEQ 80:91 REMARK 3 ) REMARK 3 SELECTION : CHAIN D AND (RESSEQ 10:74 OR RESSEQ 80:91 REMARK 3 ) REMARK 3 ATOM PAIRS NUMBER : 611 REMARK 3 RMSD : 0.691 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RESIDUE 75 MISSING FROM CHAIN C. REMARK 4 REMARK 4 2WP0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1290040625. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-AUG-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17498 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.670 REMARK 200 RESOLUTION RANGE LOW (A) : 50.770 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.100 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.67 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.55000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.700 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 2UVP REMARK 200 REMARK 200 REMARK: A COMBINATION OF 2UVP FOR HOBA AND A HOMOLGY MODEL FOR REMARK 200 DNAA I-II WAS USED FOR MOLECULAR REPLACEMENT. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS-HCL PH 8.0, 200 MM K REMARK 280 -ACETATE, 19-22% PEG 3350 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z 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 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 63.28000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.75000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 63.28000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 27.75000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 22070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 48030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -381.2 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 C 1 REMARK 465 ASP C 2 REMARK 465 THR C 3 REMARK 465 ASN C 4 REMARK 465 ASN C 5 REMARK 465 VAL C 75 REMARK 465 LYS C 92 REMARK 465 ILE C 93 REMARK 465 GLN C 94 REMARK 465 ILE C 95 REMARK 465 ASN C 96 REMARK 465 ALA C 97 REMARK 465 GLN C 98 REMARK 465 SER C 99 REMARK 465 ASN C 100 REMARK 465 ILE C 101 REMARK 465 ASN C 102 REMARK 465 TYR C 103 REMARK 465 LYS C 104 REMARK 465 ALA C 105 REMARK 465 ILE C 106 REMARK 465 LYS C 107 REMARK 465 THR C 108 REMARK 465 SER C 109 REMARK 465 VAL C 110 REMARK 465 LYS C 111 REMARK 465 ASP C 112 REMARK 465 MET D 1 REMARK 465 ASP D 2 REMARK 465 THR D 3 REMARK 465 ASN D 4 REMARK 465 LYS D 92 REMARK 465 ILE D 93 REMARK 465 GLN D 94 REMARK 465 ILE D 95 REMARK 465 ASN D 96 REMARK 465 ALA D 97 REMARK 465 GLN D 98 REMARK 465 SER D 99 REMARK 465 ASN D 100 REMARK 465 ILE D 101 REMARK 465 ASN D 102 REMARK 465 TYR D 103 REMARK 465 LYS D 104 REMARK 465 ALA D 105 REMARK 465 ILE D 106 REMARK 465 LYS D 107 REMARK 465 THR D 108 REMARK 465 SER D 109 REMARK 465 VAL D 110 REMARK 465 LYS D 111 REMARK 465 ASP D 112 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 C 201 O HOH C 202 0.81 REMARK 500 NZ LYS C 20 O HOH C 201 1.05 REMARK 500 O SER B 31 O HOH B 301 1.46 REMARK 500 NZ LYS C 20 O HOH C 202 1.53 REMARK 500 O SER A 57 O HOH A 301 2.15 REMARK 500 O LYS A 9 NH2 ARG B 30 2.16 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 NA NA A 204 NA NA B 207 2555 1.09 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 LEU B 28 N - CA - C ANGL. DEV. = -16.6 DEGREES REMARK 500 LEU C 66 CA - CB - CG ANGL. DEV. = -14.2 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 LEU A 28 49.68 -83.13 REMARK 500 GLU A 29 -4.14 175.01 REMARK 500 ARG A 30 72.19 -20.00 REMARK 500 SER A 31 -159.68 -66.14 REMARK 500 LYS A 75 -115.17 57.45 REMARK 500 LYS A 93 -85.25 -126.10 REMARK 500 ASP A 95 86.76 103.48 REMARK 500 ASN A 109 73.59 -155.61 REMARK 500 SER A 129 -171.50 -62.45 REMARK 500 PHE A 134 83.36 -152.48 REMARK 500 GLU B 29 10.98 80.37 REMARK 500 LYS B 75 -114.71 57.03 REMARK 500 LYS B 93 -85.24 -126.47 REMARK 500 ASP B 95 88.23 102.74 REMARK 500 ASN B 109 70.44 -155.73 REMARK 500 SER B 129 -171.99 -61.62 REMARK 500 PHE B 134 81.57 -152.86 REMARK 500 LEU B 141 -32.62 -37.20 REMARK 500 GLU C 10 -19.51 -26.98 REMARK 500 LYS C 20 8.56 -67.92 REMARK 500 TYR C 29 -72.17 -112.18 REMARK 500 ALA C 39 -173.17 58.03 REMARK 500 SER C 40 105.89 72.34 REMARK 500 LYS C 41 59.49 -141.36 REMARK 500 SER C 42 -12.86 58.77 REMARK 500 GLU C 68 -83.57 -43.62 REMARK 500 ILE C 69 -48.51 -26.02 REMARK 500 MET C 77 34.91 76.07 REMARK 500 HIS C 78 54.91 -159.73 REMARK 500 LEU C 79 48.51 -90.50 REMARK 500 SER C 82 29.79 -153.46 REMARK 500 VAL C 83 128.97 -34.92 REMARK 500 GLU D 8 -78.11 -45.77 REMARK 500 LYS D 9 -44.85 -25.26 REMARK 500 PRO D 19 -72.41 -38.76 REMARK 500 LYS D 20 14.48 -69.26 REMARK 500 TYR D 29 -74.46 -114.25 REMARK 500 ALA D 39 -47.73 83.96 REMARK 500 LYS D 41 117.06 92.68 REMARK 500 SER D 42 -3.03 -147.17 REMARK 500 GLU D 68 -83.19 -44.06 REMARK 500 ILE D 69 -47.52 -26.80 REMARK 500 VAL D 75 -58.05 -161.25 REMARK 500 MET D 77 61.74 -163.04 REMARK 500 LEU D 79 -94.99 28.56 REMARK 500 ALA D 80 75.17 23.19 REMARK 500 HIS D 81 7.22 -65.25 REMARK 500 SER D 82 27.20 -155.72 REMARK 500 VAL D 83 129.87 -33.87 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 MET D 77 HIS D 78 -144.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 208 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 156 OD1 REMARK 620 2 HOH B 315 O 158.9 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1181 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1182 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 1188 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1183 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1181 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 1189 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1184 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1185 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 1182 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1186 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1187 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 1184 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 1185 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 1186 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 1187 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1188 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 1190 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1189 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2UVP RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HOBA (HP1230)FROM HELICOBACTER PYLORI REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE ACCESSION NUMBER IS FOR THE FULL LENGTH PROTEIN DBREF 2WP0 A 1 180 UNP O25828 O25828_HELPY 1 180 DBREF 2WP0 B 1 180 UNP O25828 O25828_HELPY 1 180 DBREF 2WP0 C 1 112 UNP O26057 DNAA_HELPY 1 112 DBREF 2WP0 D 1 112 UNP O26057 DNAA_HELPY 1 112 SEQADV 2WP0 ILE A 12 UNP O25828 VAL 12 CONFLICT SEQADV 2WP0 ILE B 12 UNP O25828 VAL 12 CONFLICT SEQRES 1 A 180 MET LYS ASN PHE TYR ASP TRP ILE LYS GLU PHE ILE ARG SEQRES 2 A 180 ASP GLN GLY GLU PHE ILE ALA GLN GLN SER GLY TRP LEU SEQRES 3 A 180 GLU LEU GLU ARG SER SER TYR ALA LYS LEU ILE ALA GLN SEQRES 4 A 180 THR ILE SER HIS VAL LEU ASN GLY GLY SER LEU LEU VAL SEQRES 5 A 180 SER ALA ASP SER SER ARG HIS TRP PHE LEU ASN TYR ILE SEQRES 6 A 180 LEU SER ASN LEU ASN PRO LYS ASP LEU LYS GLU ARG PRO SEQRES 7 A 180 LEU LEU SER VAL ILE ASP PHE ASN ALA SER SER PHE TYR SEQRES 8 A 180 PRO LYS ASN ASP ALA ASN LEU SER LEU ALA THR ILE GLU SEQRES 9 A 180 MET THR TYR GLN ASN PRO MET PHE TRP HIS VAL GLY LYS SEQRES 10 A 180 ILE GLU ASN GLU GLY LEU LYS THR ILE LEU LEU SER LYS SEQRES 11 A 180 ILE PRO SER PHE LEU TRP LEU PHE GLU GLU LEU LYS GLU SEQRES 12 A 180 ASP CYS LEU LEU LEU LYS GLU HIS ASP SER LEU LEU ASP SEQRES 13 A 180 TYR LYS LEU LEU GLN LEU PHE LYS LEU PHE GLU ASN ALA SEQRES 14 A 180 LEU PHE SER VAL LEU TYR ASN LYS VAL THR LEU SEQRES 1 B 180 MET LYS ASN PHE TYR ASP TRP ILE LYS GLU PHE ILE ARG SEQRES 2 B 180 ASP GLN GLY GLU PHE ILE ALA GLN GLN SER GLY TRP LEU SEQRES 3 B 180 GLU LEU GLU ARG SER SER TYR ALA LYS LEU ILE ALA GLN SEQRES 4 B 180 THR ILE SER HIS VAL LEU ASN GLY GLY SER LEU LEU VAL SEQRES 5 B 180 SER ALA ASP SER SER ARG HIS TRP PHE LEU ASN TYR ILE SEQRES 6 B 180 LEU SER ASN LEU ASN PRO LYS ASP LEU LYS GLU ARG PRO SEQRES 7 B 180 LEU LEU SER VAL ILE ASP PHE ASN ALA SER SER PHE TYR SEQRES 8 B 180 PRO LYS ASN ASP ALA ASN LEU SER LEU ALA THR ILE GLU SEQRES 9 B 180 MET THR TYR GLN ASN PRO MET PHE TRP HIS VAL GLY LYS SEQRES 10 B 180 ILE GLU ASN GLU GLY LEU LYS THR ILE LEU LEU SER LYS SEQRES 11 B 180 ILE PRO SER PHE LEU TRP LEU PHE GLU GLU LEU LYS GLU SEQRES 12 B 180 ASP CYS LEU LEU LEU LYS GLU HIS ASP SER LEU LEU ASP SEQRES 13 B 180 TYR LYS LEU LEU GLN LEU PHE LYS LEU PHE GLU ASN ALA SEQRES 14 B 180 LEU PHE SER VAL LEU TYR ASN LYS VAL THR LEU SEQRES 1 C 112 MET ASP THR ASN ASN ASN ILE GLU LYS GLU ILE LEU ALA SEQRES 2 C 112 LEU VAL LYS GLN ASN PRO LYS VAL SER LEU ILE GLU TYR SEQRES 3 C 112 GLU ASN TYR PHE SER GLN LEU LYS TYR ASN PRO ASN ALA SEQRES 4 C 112 SER LYS SER ASP ILE ALA PHE PHE TYR ALA PRO ASN GLN SEQRES 5 C 112 VAL LEU CYS THR THR ILE THR ALA LYS TYR GLY ALA LEU SEQRES 6 C 112 LEU LYS GLU ILE LEU SER GLN ASN LYS VAL GLY MET HIS SEQRES 7 C 112 LEU ALA HIS SER VAL ASP VAL ARG ILE GLU VAL ALA PRO SEQRES 8 C 112 LYS ILE GLN ILE ASN ALA GLN SER ASN ILE ASN TYR LYS SEQRES 9 C 112 ALA ILE LYS THR SER VAL LYS ASP SEQRES 1 D 112 MET ASP THR ASN ASN ASN ILE GLU LYS GLU ILE LEU ALA SEQRES 2 D 112 LEU VAL LYS GLN ASN PRO LYS VAL SER LEU ILE GLU TYR SEQRES 3 D 112 GLU ASN TYR PHE SER GLN LEU LYS TYR ASN PRO ASN ALA SEQRES 4 D 112 SER LYS SER ASP ILE ALA PHE PHE TYR ALA PRO ASN GLN SEQRES 5 D 112 VAL LEU CYS THR THR ILE THR ALA LYS TYR GLY ALA LEU SEQRES 6 D 112 LEU LYS GLU ILE LEU SER GLN ASN LYS VAL GLY MET HIS SEQRES 7 D 112 LEU ALA HIS SER VAL ASP VAL ARG ILE GLU VAL ALA PRO SEQRES 8 D 112 LYS ILE GLN ILE ASN ALA GLN SER ASN ILE ASN TYR LYS SEQRES 9 D 112 ALA ILE LYS THR SER VAL LYS ASP HET CL A 201 1 HET GOL A 202 6 HET CL A 203 1 HET NA A 204 1 HET NA A 205 1 HET NA A 206 1 HET CL A 207 1 HET CL B 201 1 HET NA B 202 1 HET GOL B 203 6 HET NA B 204 1 HET CL B 205 1 HET NA B 206 1 HET NA B 207 1 HET NA B 208 1 HET NA B 209 1 HET CL B 210 1 HET NA B 211 1 HET NA B 212 1 HET ACT B 213 4 HETNAM CL CHLORIDE ION HETNAM GOL GLYCEROL HETNAM NA SODIUM ION HETNAM ACT ACETATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 CL 6(CL 1-) FORMUL 6 GOL 2(C3 H8 O3) FORMUL 8 NA 11(NA 1+) FORMUL 24 ACT C2 H3 O2 1- FORMUL 25 HOH *107(H2 O) HELIX 1 1 ASN A 3 GLN A 15 1 13 HELIX 2 2 GLU A 17 SER A 23 1 7 HELIX 3 3 SER A 32 ASN A 46 1 15 HELIX 4 4 ARG A 58 ASN A 70 1 13 HELIX 5 5 ASP A 95 TYR A 107 1 13 HELIX 6 6 LEU A 123 LEU A 128 1 6 HELIX 7 7 LEU A 154 TYR A 175 1 22 HELIX 8 8 PHE B 4 GLN B 15 1 12 HELIX 9 9 GLU B 17 SER B 23 1 7 HELIX 10 10 SER B 32 ASN B 46 1 15 HELIX 11 11 ARG B 58 ASN B 70 1 13 HELIX 12 12 ASP B 95 TYR B 107 1 13 HELIX 13 13 LEU B 123 LEU B 128 1 6 HELIX 14 14 LEU B 154 TYR B 175 1 22 HELIX 15 15 ASN C 6 LYS C 9 5 4 HELIX 16 16 GLU C 10 GLN C 17 1 8 HELIX 17 17 SER C 22 TYR C 29 1 8 HELIX 18 18 PHE C 30 LEU C 33 5 4 HELIX 19 19 ASN C 51 TYR C 62 1 12 HELIX 20 20 ALA C 64 GLN C 72 1 9 HELIX 21 21 ASN D 5 GLN D 17 1 13 HELIX 22 22 SER D 22 TYR D 29 1 8 HELIX 23 23 PHE D 30 LEU D 33 5 4 HELIX 24 24 ASN D 51 TYR D 62 1 12 HELIX 25 25 ALA D 64 GLN D 72 1 9 SHEET 1 AA 5 VAL A 82 ASP A 84 0 SHEET 2 AA 5 LEU A 50 ALA A 54 1 O LEU A 50 N ILE A 83 SHEET 3 AA 5 MET A 111 VAL A 115 1 O MET A 111 N LEU A 51 SHEET 4 AA 5 SER A 133 LEU A 137 1 O PHE A 134 N HIS A 114 SHEET 5 AA 5 LEU A 146 LEU A 147 1 O LEU A 146 N LEU A 137 SHEET 1 AB 2 VAL A 178 THR A 179 0 SHEET 2 AB 2 LYS B 2 ASN B 3 1 O LYS B 2 N THR A 179 SHEET 1 BA 5 VAL B 82 ASP B 84 0 SHEET 2 BA 5 LEU B 50 ALA B 54 1 O LEU B 50 N ILE B 83 SHEET 3 BA 5 MET B 111 VAL B 115 1 O MET B 111 N LEU B 51 SHEET 4 BA 5 SER B 133 LEU B 137 1 O PHE B 134 N HIS B 114 SHEET 5 BA 5 LEU B 146 LEU B 147 1 O LEU B 146 N LEU B 137 SHEET 1 CA 3 LYS C 34 TYR C 35 0 SHEET 2 CA 3 ILE C 44 ALA C 49 -1 O TYR C 48 N LYS C 34 SHEET 3 CA 3 ASP C 84 VAL C 89 1 O ASP C 84 N ALA C 45 SHEET 1 DA 3 LYS D 34 TYR D 35 0 SHEET 2 DA 3 ILE D 44 ALA D 49 -1 O TYR D 48 N LYS D 34 SHEET 3 DA 3 ASP D 84 VAL D 89 1 O ASP D 84 N ALA D 45 LINK OH TYR A 107 NA NA B 207 1555 2555 2.82 LINK NA NA A 204 OH TYR B 107 2555 1555 2.85 LINK OD1 ASP B 156 NA NA B 208 1555 1555 3.11 LINK OE1 GLU B 167 NA NA B 209 1555 1555 3.16 LINK NA NA B 208 O HOH B 315 1555 1555 2.96 CISPEP 1 LYS D 41 SER D 42 0 -7.82 SITE 1 AC1 1 NA B 202 SITE 1 AC2 1 ASN A 120 SITE 1 AC3 1 NA B 212 SITE 1 AC4 4 ILE A 118 GLU A 119 ASN A 120 GLU A 121 SITE 1 AC5 4 ILE B 118 GLU B 119 ASN B 120 GLU B 121 SITE 1 AC6 2 LYS B 2 GLU B 10 SITE 1 AC7 2 TYR A 91 LYS A 93 SITE 1 AC8 4 ILE A 83 TYR A 107 TYR B 107 NA B 207 SITE 1 AC9 1 SER B 153 SITE 1 BC1 1 GLU A 139 SITE 1 BC2 1 LYS A 93 SITE 1 BC3 3 ALA B 54 SER B 56 GLU B 119 SITE 1 BC4 4 TYR A 107 NA A 204 ILE B 83 TYR B 107 SITE 1 BC5 3 TRP B 60 ASP B 156 HOH B 315 SITE 1 BC6 3 ASN B 68 LYS B 164 GLU B 167 SITE 1 BC7 2 ARG A 58 HOH A 342 SITE 1 BC8 1 CL B 210 SITE 1 BC9 1 CL B 201 CRYST1 126.560 55.500 96.830 90.00 97.55 90.00 C 1 2 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 0.007901 0.000000 0.001047 0.00000 SCALE2 0.000000 0.018018 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010418 0.00000