HEADER HYDROLASE 06-MAR-03 1OPX TITLE CRYSTAL STRUCTURE OF THE TRAFFIC ATPASE (HP0525) OF THE HELICOBACTER TITLE 2 PYLORI TYPE IV SECRETION SYSTEM BOUND BY SULFATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: VIRB11 HOMOLOG; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: TRAFFIC ATPASE; COMPND 5 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, SULFATE, 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 4 30-OCT-24 1OPX 1 REMARK SEQADV SHEET LINK REVDAT 3 13-JUL-11 1OPX 1 VERSN REVDAT 2 24-FEB-09 1OPX 1 VERSN REVDAT 1 06-MAY-03 1OPX 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) : 29.63 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) (%) : 72.3 REMARK 3 NUMBER OF REFLECTIONS : 15591 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) : 0.250 REMARK 3 FREE R VALUE : 0.324 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 728 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.012 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) : 2.98 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 65.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2206 REMARK 3 BIN R VALUE (WORKING SET) : 0.3040 REMARK 3 BIN FREE R VALUE : 0.3940 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 99 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5067 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 38 REMARK 3 SOLVENT ATOMS : 23 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.78000 REMARK 3 B22 (A**2) : 2.78000 REMARK 3 B33 (A**2) : -5.57000 REMARK 3 B12 (A**2) : 0.67000 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) : 0.37 REMARK 3 ESD FROM SIGMAA (A) : 0.38 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) : 0.55 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.50 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.820 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) : 1.550 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.560 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.260 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.430 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.39 REMARK 3 BSOL : 41.85 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 : NULL REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : 9PEG.PARAM REMARK 3 PARAMETER FILE 5 : SO4-HICUP.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : 9PEG.TOPO REMARK 3 TOPOLOGY FILE 5 : SO4-HICUP.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1OPX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-MAR-03. REMARK 100 THE DEPOSITION ID IS D_1000018546. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-SEP-00 REMARK 200 TEMPERATURE (KELVIN) : 100 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 : CCD REMARK 200 DETECTOR MANUFACTURER : CUSTOM-MADE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18699 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 (%) : 87.0 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11500 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.89 REMARK 200 COMPLETENESS FOR SHELL (%) : 66.0 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: 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 (%): 56.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, PEG 400, TRIS-HCL, REMARK 280 PH 7.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 115.12000 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 115.12000 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 115.12000 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 115.12000 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 115.12000 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 115.12000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 HECAMERIC 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 24760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 78830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -184.0 KCAL/MOL 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 55.64000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 96.37131 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -55.64000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 96.37131 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DODECAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 52740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 154430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -397.0 KCAL/MOL 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 55.64000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 96.37131 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -55.64000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 96.37131 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.500000 -0.866025 0.000000 55.64000 REMARK 350 BIOMT2 4 -0.866025 -0.500000 0.000000 96.37131 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 115.12000 REMARK 350 BIOMT1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 -1.000000 115.12000 REMARK 350 BIOMT1 6 0.500000 0.866025 0.000000 -55.64000 REMARK 350 BIOMT2 6 0.866025 -0.500000 0.000000 96.37131 REMARK 350 BIOMT3 6 0.000000 0.000000 -1.000000 115.12000 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 1001 REMARK 465 THR B 1002 REMARK 465 GLU B 1003 REMARK 465 ASP B 1004 REMARK 465 ARG B 1005 REMARK 465 HIS B 1329 REMARK 465 ARG B 1330 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 LYS A 11 CG CD CE NZ REMARK 470 LYS A 21 CG CD CE NZ REMARK 470 GLU A 22 CG CD OE1 OE2 REMARK 470 GLU A 34 CG CD OE1 OE2 REMARK 470 ARG A 113 CG CD NE CZ NH1 NH2 REMARK 470 SER A 136 OG 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 CG CD CE NZ REMARK 470 LYS B1011 CG CD CE NZ REMARK 470 GLU B1034 CG CD OE1 OE2 REMARK 470 ARG B1113 CG CD NE CZ NH1 NH2 REMARK 470 SER B1136 OG REMARK 470 ARG B1295 CG CD NE CZ NH1 NH2 REMARK 470 ASN B1296 CG OD1 ND2 REMARK 470 ILE B1297 CG1 CG2 CD1 REMARK 470 LYS B1298 CG CD CE NZ REMARK 470 GLU B1300 CG CD OE1 OE2 REMARK 470 SER B1301 OG REMARK 470 LYS B1328 CG CD CE NZ 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 15 -46.99 -28.24 REMARK 500 GLU A 22 27.24 -70.29 REMARK 500 LEU A 35 -65.07 -91.22 REMARK 500 GLU A 47 141.39 -170.10 REMARK 500 ASP A 72 46.33 -103.33 REMARK 500 PHE A 76 57.57 -101.91 REMARK 500 TYR A 99 -94.90 -127.50 REMARK 500 ASN A 101 57.60 -147.96 REMARK 500 PRO A 135 34.80 -74.10 REMARK 500 SER A 136 89.63 19.05 REMARK 500 THR A 138 149.95 176.84 REMARK 500 ASN A 156 50.16 -109.20 REMARK 500 GLU A 209 -46.85 -149.40 REMARK 500 GLU A 248 128.73 -170.42 REMARK 500 ARG A 250 -66.04 -101.46 REMARK 500 SER A 251 -33.85 -178.59 REMARK 500 ALA A 254 -67.34 -22.86 REMARK 500 LYS A 266 -110.82 -24.28 REMARK 500 GLU A 324 128.96 -177.90 REMARK 500 GLU B1015 -47.54 -27.50 REMARK 500 GLU B1022 23.07 -65.27 REMARK 500 LEU B1035 -67.37 -91.54 REMARK 500 GLU B1047 138.74 -172.04 REMARK 500 ASP B1072 46.91 -103.54 REMARK 500 PHE B1076 57.44 -101.09 REMARK 500 TYR B1099 -93.70 -125.51 REMARK 500 ASN B1101 58.11 -146.00 REMARK 500 SER B1136 72.50 58.93 REMARK 500 LYS B1137 86.86 -69.69 REMARK 500 ASN B1156 49.56 -105.80 REMARK 500 GLU B1209 -48.27 -149.56 REMARK 500 ARG B1250 -66.37 -100.84 REMARK 500 SER B1251 -32.38 -178.20 REMARK 500 ALA B1254 -67.30 -22.79 REMARK 500 LYS B1266 -111.56 -21.74 REMARK 500 GLU B1324 128.13 -178.71 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 SO4 A 4000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 5000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2PE B 2000 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1G6O RELATED DB: PDB REMARK 900 RELATED ID: 1NLY RELATED DB: PDB REMARK 900 RELATED ID: 1NLZ RELATED DB: PDB DBREF 1OPX A 1 330 UNP Q7BK04 Q7BK04_HELPY 1 330 DBREF 1OPX B 1001 1330 UNP Q7BK04 Q7BK04_HELPY 1 330 SEQADV 1OPX MSE A 42 UNP Q7BK04 MET 42 MODIFIED RESIDUE SEQADV 1OPX MSE A 82 UNP Q7BK04 MET 82 MODIFIED RESIDUE SEQADV 1OPX MSE A 192 UNP Q7BK04 MET 192 MODIFIED RESIDUE SEQADV 1OPX MSE A 239 UNP Q7BK04 MET 239 MODIFIED RESIDUE SEQADV 1OPX MSE A 287 UNP Q7BK04 MET 287 MODIFIED RESIDUE SEQADV 1OPX MSE A 312 UNP Q7BK04 MET 312 MODIFIED RESIDUE SEQADV 1OPX MSE B 1042 UNP Q7BK04 MET 42 MODIFIED RESIDUE SEQADV 1OPX MSE B 1082 UNP Q7BK04 MET 82 MODIFIED RESIDUE SEQADV 1OPX MSE B 1192 UNP Q7BK04 MET 192 MODIFIED RESIDUE SEQADV 1OPX MSE B 1239 UNP Q7BK04 MET 239 MODIFIED RESIDUE SEQADV 1OPX MSE B 1287 UNP Q7BK04 MET 287 MODIFIED RESIDUE SEQADV 1OPX MSE B 1312 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 1OPX MSE A 42 MET SELENOMETHIONINE MODRES 1OPX MSE A 82 MET SELENOMETHIONINE MODRES 1OPX MSE A 192 MET SELENOMETHIONINE MODRES 1OPX MSE A 239 MET SELENOMETHIONINE MODRES 1OPX MSE A 287 MET SELENOMETHIONINE MODRES 1OPX MSE A 312 MET SELENOMETHIONINE MODRES 1OPX MSE B 1042 MET SELENOMETHIONINE MODRES 1OPX MSE B 1082 MET SELENOMETHIONINE MODRES 1OPX MSE B 1192 MET SELENOMETHIONINE MODRES 1OPX MSE B 1239 MET SELENOMETHIONINE MODRES 1OPX MSE B 1287 MET SELENOMETHIONINE MODRES 1OPX MSE B 1312 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 B1042 8 HET MSE B1082 8 HET MSE B1192 8 HET MSE B1239 8 HET MSE B1287 8 HET MSE B1312 8 HET SO4 A4000 5 HET SO4 B5000 5 HET 2PE B2000 28 HETNAM MSE SELENOMETHIONINE HETNAM SO4 SULFATE ION HETNAM 2PE NONAETHYLENE GLYCOL FORMUL 1 MSE 12(C5 H11 N O2 SE) FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 2PE C18 H38 O10 FORMUL 6 HOH *23(H2 O) HELIX 1 1 LEU A 6 GLU A 22 1 17 HELIX 2 2 ALA A 24 LYS A 41 1 18 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 MSE A 192 1 10 HELIX 8 8 GLU A 193 ILE A 195 5 3 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 SER A 290 1 15 HELIX 12 12 ASN A 291 ARG A 295 5 5 HELIX 13 13 LYS A 298 ILE A 310 1 13 HELIX 14 14 LEU B 1006 GLU B 1022 1 17 HELIX 15 15 ALA B 1024 LYS B 1041 1 18 HELIX 16 16 ARG B 1073 PHE B 1076 5 4 HELIX 17 17 SER B 1077 LYS B 1092 1 16 HELIX 18 18 PRO B 1141 GLN B 1148 1 8 HELIX 19 19 ASN B 1156 ILE B 1170 1 15 HELIX 20 20 GLY B 1183 MSE B 1192 1 10 HELIX 21 21 GLU B 1193 ILE B 1195 5 3 HELIX 22 22 THR B 1228 LEU B 1237 1 10 HELIX 23 23 SER B 1251 SER B 1263 1 13 HELIX 24 24 SER B 1276 SER B 1290 1 15 HELIX 25 25 ASN B 1291 ARG B 1295 5 5 HELIX 26 26 LYS B 1298 ILE B 1310 1 13 SHEET 1 A 5 TRP A 65 ASP A 69 0 SHEET 2 A 5 VAL A 55 LYS A 60 -1 N VAL A 58 O GLN A 66 SHEET 3 A 5 ILE A 45 ASN A 51 -1 N CYS A 49 O TRP A 57 SHEET 4 A 5 SER A 129 ARG A 133 -1 O ILE A 132 N ILE A 48 SHEET 5 A 5 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 SER A 203 O LEU A 221 SHEET 3 B 7 ARG A 243 LEU A 246 1 O ILE A 245 N ILE A 204 SHEET 4 B 7 GLY A 267 LEU A 272 1 O GLY A 267 N ILE A 244 SHEET 5 B 7 VAL A 174 GLY A 178 1 N VAL A 176 O THR A 270 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 TYR A 326 N ILE A 313 SHEET 1 C 5 TRP B1065 ASP B1069 0 SHEET 2 C 5 VAL B1055 LYS B1060 -1 N VAL B1058 O GLN B1066 SHEET 3 C 5 ILE B1045 ASN B1051 -1 N CYS B1049 O TRP B1057 SHEET 4 C 5 SER B1129 ARG B1133 -1 O ILE B1132 N ILE B1048 SHEET 5 C 5 ILE B1103 ASN B1107 -1 N SER B1106 O VAL B1114 SHEET 1 D 7 TYR B1218 PHE B1222 0 SHEET 2 D 7 ILE B1201 GLU B1205 1 N SER B1203 O LEU B1221 SHEET 3 D 7 ARG B1243 LEU B1246 1 O ILE B1245 N ILE B1204 SHEET 4 D 7 GLY B1267 LEU B1272 1 O GLY B1267 N ILE B1244 SHEET 5 D 7 VAL B1174 GLY B1178 1 N VAL B1176 O THR B1270 SHEET 6 D 7 MSE B1312 ILE B1316 1 O VAL B1314 N CYS B1177 SHEET 7 D 7 CYS B1322 ILE B1327 -1 O TYR B1326 N ILE B1313 LINK C LYS A 41 N MSE A 42 1555 1555 1.32 LINK C MSE A 42 N GLU A 43 1555 1555 1.34 LINK C LEU A 81 N MSE A 82 1555 1555 1.32 LINK C MSE A 82 N HIS A 83 1555 1555 1.32 LINK C ILE A 191 N MSE A 192 1555 1555 1.33 LINK C MSE A 192 N GLU A 193 1555 1555 1.33 LINK C ARG A 238 N MSE A 239 1555 1555 1.33 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 1.34 LINK C LYS B1041 N MSE B1042 1555 1555 1.33 LINK C MSE B1042 N GLU B1043 1555 1555 1.34 LINK C LEU B1081 N MSE B1082 1555 1555 1.33 LINK C MSE B1082 N HIS B1083 1555 1555 1.32 LINK C ILE B1191 N MSE B1192 1555 1555 1.34 LINK C MSE B1192 N GLU B1193 1555 1555 1.33 LINK C ARG B1238 N MSE B1239 1555 1555 1.33 LINK C MSE B1239 N ARG B1240 1555 1555 1.33 LINK C ASN B1286 N MSE B1287 1555 1555 1.33 LINK C MSE B1287 N SER B1288 1555 1555 1.32 LINK C ASP B1311 N MSE B1312 1555 1555 1.33 LINK C MSE B1312 N ILE B1313 1555 1555 1.33 CISPEP 1 SER A 119 PRO A 120 0 2.86 CISPEP 2 SER B 1119 PRO B 1120 0 1.28 SITE 1 AC1 9 ARG A 133 GLY A 179 THR A 180 GLY A 181 SITE 2 AC1 9 SER A 182 GLY A 183 LYS A 184 THR A 185 SITE 3 AC1 9 HOH A3004 SITE 1 AC2 8 ARG B1133 THR B1180 GLY B1181 SER B1182 SITE 2 AC2 8 GLY B1183 LYS B1184 THR B1185 HOH B3007 SITE 1 AC3 12 ASP A 38 LYS A 41 PRO A 67 PHE A 68 SITE 2 AC3 12 ASP A 69 ARG A 73 ASP B1038 LYS B1041 SITE 3 AC3 12 PRO B1067 PHE B1068 ASP B1069 ARG B1073 CRYST1 111.280 111.280 230.240 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 0.008986 0.005188 0.000000 0.00000 SCALE2 0.000000 0.010377 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004343 0.00000