HEADER HYDROLASE 08-JAN-03 1NLY TITLE CRYSTAL STRUCTURE OF THE TRAFFIC ATPASE OF THE HELICOBACTER PYLORI TITLE 2 TYPE IV SECRETION SYSTEM IN COMPLEX WITH ATPGAMMAS COMPND MOL_ID: 1; COMPND 2 MOLECULE: VIRB11 HOMOLOG; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI; SOURCE 3 ORGANISM_TAXID: 85962; SOURCE 4 STRAIN: 26695; SOURCE 5 GENE: HP0525; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS VIRB11 ATPASE, BACTERIAL TYPE IV SECRETION, ATPGAMMAS, HP0525, KEYWDS 2 HELICOBACTER PYLORI, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.N.SAVVIDES,H.J.YEO,M.R.BECK,F.BLAESING,R.LURZ,E.LANKA,R.BUHRDORF, AUTHOR 2 W.FISCHER,R.HAAS,G.WAKSMAN REVDAT 5 16-OCT-24 1NLY 1 REMARK SEQADV LINK REVDAT 4 07-MAR-12 1NLY 1 HET HETATM HETNAM HETSYN REVDAT 3 13-JUL-11 1NLY 1 VERSN REVDAT 2 24-FEB-09 1NLY 1 VERSN REVDAT 1 06-MAY-03 1NLY 0 JRNL AUTH S.N.SAVVIDES,H.J.YEO,M.R.BECK,F.BLAESING,R.LURZ,E.LANKA, JRNL AUTH 2 R.BUHRDORF,W.FISCHER,R.HAAS,G.WAKSMAN JRNL TITL VIRB11 ATPASES ARE DYNAMIC HEXAMERIC ASSEMBLIES: NEW JRNL TITL 2 INSIGHTS INTO BACTERIAL TYPE IV SECRETION JRNL REF EMBO J. V. 22 1969 2003 JRNL REFN ISSN 0261-4189 JRNL PMID 12727865 JRNL DOI 10.1093/EMBOJ/CDG223 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 75.4 REMARK 3 NUMBER OF REFLECTIONS : 16131 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 SET) : 0.243 REMARK 3 FREE R VALUE : 0.304 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 773 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.011 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.97 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 58.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1955 REMARK 3 BIN R VALUE (WORKING SET) : 0.2780 REMARK 3 BIN FREE R VALUE : 0.3600 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 94 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.037 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5103 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 96 REMARK 3 SOLVENT ATOMS : 42 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.93000 REMARK 3 B22 (A**2) : 1.93000 REMARK 3 B33 (A**2) : -3.86000 REMARK 3 B12 (A**2) : -1.65000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.36 REMARK 3 ESD FROM SIGMAA (A) : 0.35 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.48 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.37 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.840 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.800 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.010 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.750 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.140 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 25.38 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : ATPGS+ADP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : 9PEG.PARAM REMARK 3 PARAMETER FILE 5 : ION.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : ATPGS+ADP.TOPO REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : 9PEG.TOPO REMARK 3 TOPOLOGY FILE 5 : ION.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1NLY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JAN-03. REMARK 100 THE DEPOSITION ID IS D_1000017990. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21264 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.37800 REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, PEG 400, TRIS-HCL, REMARK 280 PH 7.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z+1/2 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 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 115.45500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 115.45500 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 115.45500 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 115.45500 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 115.45500 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 115.45500 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 300 REMARK: THE BIOLOGICALLY RELEVANT HEXAMERIC ASSEMBLY IS GENERATED REMARK 300 FROM THE DIMER IN THE ASYMMETRIC UNIT BY A CRYSTALLOGRAPHIC THREE REMARK 300 FOLD AXIS 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: HEXAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 55.41000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 95.97294 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -55.41000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 95.97294 REMARK 350 BIOMT3 3 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 THR A 2 REMARK 465 GLU A 3 REMARK 465 ASP A 4 REMARK 465 ARG A 5 REMARK 465 HIS A 329 REMARK 465 ARG A 330 REMARK 465 MET B 1 REMARK 465 THR B 2 REMARK 465 GLU B 3 REMARK 465 ASP B 4 REMARK 465 ARG B 5 REMARK 465 HIS B 329 REMARK 465 ARG B 330 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 295 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 296 CG OD1 ND2 REMARK 470 LYS A 298 CG CD CE NZ REMARK 470 GLU A 300 CG CD OE1 OE2 REMARK 470 SER A 301 OG REMARK 470 LYS A 328 O CG CD CE NZ REMARK 470 ARG B 295 CG CD NE CZ NH1 NH2 REMARK 470 ASN B 296 CG OD1 ND2 REMARK 470 ILE B 297 CG1 CG2 CD1 REMARK 470 LYS B 298 CG CD CE NZ REMARK 470 GLU B 300 CG CD OE1 OE2 REMARK 470 SER B 301 OG REMARK 470 LYS B 328 O CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ASN A 226 CB ASN A 226 CG -0.148 REMARK 500 ASN B 226 CB ASN B 226 CG -0.151 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 ASN A 226 CB - CA - C ANGL. DEV. = -12.4 DEGREES REMARK 500 ARG A 250 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG B 250 NE - CZ - NH1 ANGL. DEV. = 3.3 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 GLU A 22 3.14 -66.46 REMARK 500 LEU A 35 -76.59 -88.15 REMARK 500 ASP A 72 66.37 -111.14 REMARK 500 PHE A 76 51.66 -118.93 REMARK 500 TYR A 99 -94.41 -125.79 REMARK 500 ASN A 101 68.38 -119.76 REMARK 500 SER A 106 -155.66 -159.17 REMARK 500 PRO A 135 -174.51 -62.26 REMARK 500 ASN A 156 53.31 -97.84 REMARK 500 ILE A 191 0.25 -67.99 REMARK 500 LYS A 197 -8.75 -56.18 REMARK 500 GLU A 209 -38.49 -141.80 REMARK 500 LEU A 237 2.53 -62.90 REMARK 500 ARG A 250 -64.30 -107.54 REMARK 500 SER A 251 -34.33 176.83 REMARK 500 ALA A 254 -70.10 -26.93 REMARK 500 LYS A 266 -122.99 -35.10 REMARK 500 SER A 276 -179.54 -179.15 REMARK 500 GLU B 15 -54.69 -29.49 REMARK 500 GLU B 22 5.80 -68.28 REMARK 500 LEU B 35 -75.71 -89.28 REMARK 500 ASP B 72 66.83 -109.20 REMARK 500 PHE B 76 50.71 -118.06 REMARK 500 TYR B 99 -92.61 -128.31 REMARK 500 ASN B 101 66.82 -118.56 REMARK 500 SER B 106 -154.94 -158.65 REMARK 500 PRO B 135 -179.09 -65.07 REMARK 500 ASN B 156 51.74 -95.05 REMARK 500 ILE B 191 2.03 -69.14 REMARK 500 PRO B 196 125.29 -38.69 REMARK 500 LYS B 197 -9.45 -54.82 REMARK 500 GLU B 209 -39.53 -141.71 REMARK 500 LEU B 237 1.79 -63.18 REMARK 500 ARG B 250 -64.66 -106.83 REMARK 500 SER B 251 -35.79 176.65 REMARK 500 ALA B 254 -70.62 -24.54 REMARK 500 LYS B 266 -118.48 -37.74 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 MG A 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 185 OG1 REMARK 620 2 AGS A 402 O2B 92.6 REMARK 620 3 HOH A1022 O 118.8 146.8 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AGS A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AGS B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2PE B 403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1G6O RELATED DB: PDB REMARK 900 THE SAME PROTEIN (HP0525 FROM HELICOBACTER PYLORI) COMPLEXED WITH REMARK 900 ADP DBREF 1NLY A 1 330 UNP Q7BK04 Q7BK04_HELPY 1 330 DBREF 1NLY B 1 330 UNP Q7BK04 Q7BK04_HELPY 1 330 SEQADV 1NLY MSE A 42 UNP Q7BK04 MET 42 MODIFIED RESIDUE SEQADV 1NLY MSE A 82 UNP Q7BK04 MET 82 MODIFIED RESIDUE SEQADV 1NLY MSE A 192 UNP Q7BK04 MET 192 MODIFIED RESIDUE SEQADV 1NLY MSE A 239 UNP Q7BK04 MET 239 MODIFIED RESIDUE SEQADV 1NLY MSE A 287 UNP Q7BK04 MET 287 MODIFIED RESIDUE SEQADV 1NLY MSE A 312 UNP Q7BK04 MET 312 MODIFIED RESIDUE SEQADV 1NLY MSE B 42 UNP Q7BK04 MET 42 MODIFIED RESIDUE SEQADV 1NLY MSE B 82 UNP Q7BK04 MET 82 MODIFIED RESIDUE SEQADV 1NLY MSE B 192 UNP Q7BK04 MET 192 MODIFIED RESIDUE SEQADV 1NLY MSE B 239 UNP Q7BK04 MET 239 MODIFIED RESIDUE SEQADV 1NLY MSE B 287 UNP Q7BK04 MET 287 MODIFIED RESIDUE SEQADV 1NLY MSE B 312 UNP Q7BK04 MET 312 MODIFIED RESIDUE SEQRES 1 A 330 MET THR GLU ASP ARG LEU SER ALA GLU ASP LYS LYS PHE SEQRES 2 A 330 LEU GLU VAL GLU ARG ALA LEU LYS GLU ALA ALA LEU ASN SEQRES 3 A 330 PRO LEU ARG HIS ALA THR GLU GLU LEU PHE GLY ASP PHE SEQRES 4 A 330 LEU LYS MSE GLU ASN ILE THR GLU ILE CYS TYR ASN GLY SEQRES 5 A 330 ASN LYS VAL VAL TRP VAL LEU LYS ASN ASN GLY GLU TRP SEQRES 6 A 330 GLN PRO PHE ASP VAL ARG ASP ARG LYS ALA PHE SER LEU SEQRES 7 A 330 SER ARG LEU MSE HIS PHE ALA ARG CYS CYS ALA SER PHE SEQRES 8 A 330 LYS LYS LYS THR ILE ASP ASN TYR GLU ASN PRO ILE LEU SEQRES 9 A 330 SER SER ASN LEU ALA ASN GLY GLU ARG VAL GLN ILE VAL SEQRES 10 A 330 LEU SER PRO VAL THR VAL ASN ASP GLU THR ILE SER ILE SEQRES 11 A 330 SER ILE ARG ILE PRO SER LYS THR THR TYR PRO HIS SER SEQRES 12 A 330 PHE PHE GLU GLU GLN GLY PHE TYR ASN LEU LEU ASP ASN SEQRES 13 A 330 LYS GLU GLN ALA ILE SER ALA ILE LYS ASP GLY ILE ALA SEQRES 14 A 330 ILE GLY LYS ASN VAL ILE VAL CYS GLY GLY THR GLY SER SEQRES 15 A 330 GLY LYS THR THR TYR ILE LYS SER ILE MSE GLU PHE ILE SEQRES 16 A 330 PRO LYS GLU GLU ARG ILE ILE SER ILE GLU ASP THR GLU SEQRES 17 A 330 GLU ILE VAL PHE LYS HIS HIS LYS ASN TYR THR GLN LEU SEQRES 18 A 330 PHE PHE GLY GLY ASN ILE THR SER ALA ASP CYS LEU LYS SEQRES 19 A 330 SER CYS LEU ARG MSE ARG PRO ASP ARG ILE ILE LEU GLY SEQRES 20 A 330 GLU LEU ARG SER SER GLU ALA TYR ASP PHE TYR ASN VAL SEQRES 21 A 330 LEU CYS SER GLY HIS LYS GLY THR LEU THR THR LEU HIS SEQRES 22 A 330 ALA GLY SER SER GLU GLU ALA PHE ILE ARG LEU ALA ASN SEQRES 23 A 330 MSE SER SER SER ASN SER ALA ALA ARG ASN ILE LYS PHE SEQRES 24 A 330 GLU SER LEU ILE GLU GLY PHE LYS ASP LEU ILE ASP MSE SEQRES 25 A 330 ILE VAL HIS ILE ASN HIS HIS LYS GLN CYS ASP GLU PHE SEQRES 26 A 330 TYR ILE LYS HIS ARG SEQRES 1 B 330 MET THR GLU ASP ARG LEU SER ALA GLU ASP LYS LYS PHE SEQRES 2 B 330 LEU GLU VAL GLU ARG ALA LEU LYS GLU ALA ALA LEU ASN SEQRES 3 B 330 PRO LEU ARG HIS ALA THR GLU GLU LEU PHE GLY ASP PHE SEQRES 4 B 330 LEU LYS MSE GLU ASN ILE THR GLU ILE CYS TYR ASN GLY SEQRES 5 B 330 ASN LYS VAL VAL TRP VAL LEU LYS ASN ASN GLY GLU TRP SEQRES 6 B 330 GLN PRO PHE ASP VAL ARG ASP ARG LYS ALA PHE SER LEU SEQRES 7 B 330 SER ARG LEU MSE HIS PHE ALA ARG CYS CYS ALA SER PHE SEQRES 8 B 330 LYS LYS LYS THR ILE ASP ASN TYR GLU ASN PRO ILE LEU SEQRES 9 B 330 SER SER ASN LEU ALA ASN GLY GLU ARG VAL GLN ILE VAL SEQRES 10 B 330 LEU SER PRO VAL THR VAL ASN ASP GLU THR ILE SER ILE SEQRES 11 B 330 SER ILE ARG ILE PRO SER LYS THR THR TYR PRO HIS SER SEQRES 12 B 330 PHE PHE GLU GLU GLN GLY PHE TYR ASN LEU LEU ASP ASN SEQRES 13 B 330 LYS GLU GLN ALA ILE SER ALA ILE LYS ASP GLY ILE ALA SEQRES 14 B 330 ILE GLY LYS ASN VAL ILE VAL CYS GLY GLY THR GLY SER SEQRES 15 B 330 GLY LYS THR THR TYR ILE LYS SER ILE MSE GLU PHE ILE SEQRES 16 B 330 PRO LYS GLU GLU ARG ILE ILE SER ILE GLU ASP THR GLU SEQRES 17 B 330 GLU ILE VAL PHE LYS HIS HIS LYS ASN TYR THR GLN LEU SEQRES 18 B 330 PHE PHE GLY GLY ASN ILE THR SER ALA ASP CYS LEU LYS SEQRES 19 B 330 SER CYS LEU ARG MSE ARG PRO ASP ARG ILE ILE LEU GLY SEQRES 20 B 330 GLU LEU ARG SER SER GLU ALA TYR ASP PHE TYR ASN VAL SEQRES 21 B 330 LEU CYS SER GLY HIS LYS GLY THR LEU THR THR LEU HIS SEQRES 22 B 330 ALA GLY SER SER GLU GLU ALA PHE ILE ARG LEU ALA ASN SEQRES 23 B 330 MSE SER SER SER ASN SER ALA ALA ARG ASN ILE LYS PHE SEQRES 24 B 330 GLU SER LEU ILE GLU GLY PHE LYS ASP LEU ILE ASP MSE SEQRES 25 B 330 ILE VAL HIS ILE ASN HIS HIS LYS GLN CYS ASP GLU PHE SEQRES 26 B 330 TYR ILE LYS HIS ARG MODRES 1NLY MSE A 42 MET SELENOMETHIONINE MODRES 1NLY MSE A 82 MET SELENOMETHIONINE MODRES 1NLY MSE A 192 MET SELENOMETHIONINE MODRES 1NLY MSE A 239 MET SELENOMETHIONINE MODRES 1NLY MSE A 287 MET SELENOMETHIONINE MODRES 1NLY MSE A 312 MET SELENOMETHIONINE MODRES 1NLY MSE B 42 MET SELENOMETHIONINE MODRES 1NLY MSE B 82 MET SELENOMETHIONINE MODRES 1NLY MSE B 192 MET SELENOMETHIONINE MODRES 1NLY MSE B 239 MET SELENOMETHIONINE MODRES 1NLY MSE B 287 MET SELENOMETHIONINE MODRES 1NLY MSE B 312 MET SELENOMETHIONINE HET MSE A 42 8 HET MSE A 82 8 HET MSE A 192 8 HET MSE A 239 8 HET MSE A 287 8 HET MSE A 312 8 HET MSE B 42 8 HET MSE B 82 8 HET MSE B 192 8 HET MSE B 239 8 HET MSE B 287 8 HET MSE B 312 8 HET MG A 401 1 HET AGS A 402 31 HET SO4 B 401 5 HET AGS B 402 31 HET 2PE B 403 28 HETNAM MSE SELENOMETHIONINE HETNAM MG MAGNESIUM ION HETNAM AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER HETNAM SO4 SULFATE ION HETNAM 2PE NONAETHYLENE GLYCOL HETSYN AGS ATP-GAMMA-S; ADENOSINE 5'-(3-THIOTRIPHOSPHATE); HETSYN 2 AGS ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE); ADENOSINE-5'- HETSYN 3 AGS DIPHOSPHATE MONOTHIOPHOSPHATE FORMUL 1 MSE 12(C5 H11 N O2 SE) FORMUL 3 MG MG 2+ FORMUL 4 AGS 2(C10 H16 N5 O12 P3 S) FORMUL 5 SO4 O4 S 2- FORMUL 7 2PE C18 H38 O10 FORMUL 8 HOH *42(H2 O) HELIX 1 1 LEU A 6 GLU A 22 1 17 HELIX 2 2 ALA A 24 MSE A 42 1 19 HELIX 3 3 ARG A 73 PHE A 76 5 4 HELIX 4 4 SER A 77 LYS A 92 1 16 HELIX 5 5 PRO A 141 GLN A 148 1 8 HELIX 6 6 ASN A 156 ILE A 170 1 15 HELIX 7 7 GLY A 183 ILE A 191 1 9 HELIX 8 8 MSE A 192 ILE A 195 5 4 HELIX 9 9 THR A 228 LEU A 237 1 10 HELIX 10 10 SER A 251 SER A 263 1 13 HELIX 11 11 SER A 276 ASN A 291 1 16 HELIX 12 14 LEU B 6 GLU B 22 1 17 HELIX 13 15 ALA B 24 MSE B 42 1 19 HELIX 14 16 ARG B 73 PHE B 76 5 4 HELIX 15 17 SER B 77 LYS B 92 1 16 HELIX 16 18 PRO B 141 GLN B 148 1 8 HELIX 17 19 ASN B 156 ILE B 170 1 15 HELIX 18 20 GLY B 183 ILE B 191 1 9 HELIX 19 21 MSE B 192 ILE B 195 5 4 HELIX 20 22 THR B 228 LEU B 237 1 10 HELIX 21 23 SER B 251 SER B 263 1 13 HELIX 22 24 SER B 276 ASN B 291 1 16 SHEET 1 A 6 TRP A 65 ASP A 69 0 SHEET 2 A 6 VAL A 55 LYS A 60 -1 N VAL A 56 O PHE A 68 SHEET 3 A 6 ILE A 45 ASN A 51 -1 N CYS A 49 O TRP A 57 SHEET 4 A 6 SER A 129 ARG A 133 -1 O ILE A 130 N TYR A 50 SHEET 5 A 6 ARG A 113 VAL A 117 -1 N VAL A 117 O SER A 129 SHEET 6 A 6 ILE A 103 ASN A 107 -1 N SER A 106 O VAL A 114 SHEET 1 B 7 TYR A 218 PHE A 222 0 SHEET 2 B 7 ILE A 201 GLU A 205 1 N GLU A 205 O LEU A 221 SHEET 3 B 7 ARG A 243 GLU A 248 1 O GLY A 247 N ILE A 204 SHEET 4 B 7 GLY A 267 HIS A 273 1 O GLY A 267 N ILE A 244 SHEET 5 B 7 VAL A 174 GLY A 178 1 N VAL A 174 O THR A 268 SHEET 6 B 7 MSE A 312 ILE A 316 1 O VAL A 314 N CYS A 177 SHEET 7 B 7 CYS A 322 ILE A 327 -1 O GLU A 324 N HIS A 315 SHEET 1 C 6 TRP B 65 ASP B 69 0 SHEET 2 C 6 VAL B 55 LYS B 60 -1 N VAL B 58 O GLN B 66 SHEET 3 C 6 ILE B 45 ASN B 51 -1 N CYS B 49 O TRP B 57 SHEET 4 C 6 SER B 129 ARG B 133 -1 O ILE B 132 N ILE B 48 SHEET 5 C 6 ARG B 113 VAL B 117 -1 N VAL B 117 O SER B 129 SHEET 6 C 6 ILE B 103 ASN B 107 -1 N SER B 106 O VAL B 114 SHEET 1 D 7 TYR B 218 PHE B 222 0 SHEET 2 D 7 ILE B 201 GLU B 205 1 N GLU B 205 O LEU B 221 SHEET 3 D 7 ARG B 243 GLU B 248 1 O GLY B 247 N ILE B 204 SHEET 4 D 7 GLY B 267 HIS B 273 1 O GLY B 267 N ILE B 244 SHEET 5 D 7 VAL B 174 GLY B 178 1 N VAL B 174 O THR B 268 SHEET 6 D 7 MSE B 312 ILE B 316 1 O VAL B 314 N CYS B 177 SHEET 7 D 7 CYS B 322 ILE B 327 -1 O GLU B 324 N HIS B 315 LINK C LYS A 41 N MSE A 42 1555 1555 1.32 LINK C MSE A 42 N GLU A 43 1555 1555 1.33 LINK C LEU A 81 N MSE A 82 1555 1555 1.33 LINK C MSE A 82 N HIS A 83 1555 1555 1.33 LINK C ILE A 191 N MSE A 192 1555 1555 1.33 LINK C MSE A 192 N GLU A 193 1555 1555 1.32 LINK C ARG A 238 N MSE A 239 1555 1555 1.32 LINK C MSE A 239 N ARG A 240 1555 1555 1.33 LINK C ASN A 286 N MSE A 287 1555 1555 1.33 LINK C MSE A 287 N SER A 288 1555 1555 1.33 LINK C ASP A 311 N MSE A 312 1555 1555 1.33 LINK C MSE A 312 N ILE A 313 1555 1555 1.33 LINK C LYS B 41 N MSE B 42 1555 1555 1.32 LINK C MSE B 42 N GLU B 43 1555 1555 1.33 LINK C LEU B 81 N MSE B 82 1555 1555 1.33 LINK C MSE B 82 N HIS B 83 1555 1555 1.33 LINK C ILE B 191 N MSE B 192 1555 1555 1.33 LINK C MSE B 192 N GLU B 193 1555 1555 1.33 LINK C ARG B 238 N MSE B 239 1555 1555 1.33 LINK C MSE B 239 N ARG B 240 1555 1555 1.33 LINK C ASN B 286 N MSE B 287 1555 1555 1.33 LINK C MSE B 287 N SER B 288 1555 1555 1.33 LINK C ASP B 311 N MSE B 312 1555 1555 1.33 LINK C MSE B 312 N ILE B 313 1555 1555 1.33 LINK OG1 THR A 185 MG MG A 401 1555 1555 1.72 LINK MG MG A 401 O2B AGS A 402 1555 1555 2.58 LINK MG MG A 401 O HOH A1022 1555 1555 2.64 CISPEP 1 SER A 119 PRO A 120 0 1.58 CISPEP 2 SER B 119 PRO B 120 0 -0.58 SITE 1 AC1 3 THR A 185 AGS A 402 HOH A1022 SITE 1 AC2 16 ASN A 61 ARG A 113 ARG A 133 TYR A 140 SITE 2 AC2 16 GLY A 179 THR A 180 GLY A 181 SER A 182 SITE 3 AC2 16 GLY A 183 LYS A 184 THR A 185 THR A 186 SITE 4 AC2 16 GLU A 248 HIS A 273 MG A 401 HOH A1002 SITE 1 AC3 6 GLY B 181 SER B 182 GLY B 183 LYS B 184 SITE 2 AC3 6 THR B 185 AGS B 402 SITE 1 AC4 15 ASN B 61 ARG B 133 TYR B 140 GLY B 179 SITE 2 AC4 15 THR B 180 GLY B 181 SER B 182 GLY B 183 SITE 3 AC4 15 LYS B 184 THR B 185 THR B 186 GLU B 248 SITE 4 AC4 15 HIS B 273 SO4 B 401 HOH B 506 SITE 1 AC5 12 ASP A 38 PHE A 39 LYS A 41 MSE A 42 SITE 2 AC5 12 PRO A 67 PHE A 68 ASP A 69 ARG A 73 SITE 3 AC5 12 LYS B 41 PHE B 68 ASP B 69 ARG B 73 CRYST1 110.820 110.820 230.910 90.00 90.00 120.00 P 63 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 0.009024 0.005210 0.000000 0.00000 SCALE2 0.000000 0.010420 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004331 0.00000