10 20 30 40 50 60 70 80 1SVP - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER VIRAL PROTEIN 22-MAR-96 1SVP
TITLE SINDBIS VIRUS CAPSID PROTEIN
COMPND MOL_ID: 1; COMPND 2 MOLECULE: SINDBIS VIRUS CAPSID PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: MET 106 - ALA 264 OF THE NATIVE SINDBIS CAPSID COMPND 5 PROTEIN; COMPND 6 SYNONYM: SINDBIS VIRUS COAT PROTEIN; COMPND 7 EC: 3.4.21.-; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SINDBIS VIRUS; SOURCE 3 ORGANISM_TAXID: 11034; SOURCE 4 GENE: SINDBIS VIRUS CAPSID PROTEIN; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: T7; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET11A; SOURCE 9 EXPRESSION_SYSTEM_GENE: SINDBIS VIRUS CAPSID PROTEIN; SOURCE 10 OTHER_DETAILS: T7 RNA POLYMERASE
KEYWDS SINDBIS VIRUS CAPSID PROTEIN, CHYMOTRYPSIN-LIKE SERINE, KEYWDS 2 MUTANT, COAT PROTEIN, VIRAL PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR S.LEE,M.G.ROSSMANN
REVDAT 2 24-FEB-09 1SVP 1 VERSN REVDAT 1 17-AUG-96 1SVP 0
JRNL AUTH S.LEE,K.E.OWEN,H.K.CHOI,H.LEE,G.LU,G.WENGLER, JRNL AUTH 2 D.T.BROWN,M.G.ROSSMANN,R.J.KUHN JRNL TITL IDENTIFICATION OF A PROTEIN BINDING SITE ON THE JRNL TITL 2 SURFACE OF THE ALPHAVIRUS NUCLEOCAPSID AND ITS JRNL TITL 3 IMPLICATION IN VIRUS ASSEMBLY. JRNL REF STRUCTURE V. 4 531 1996 JRNL REFN ISSN 0969-2126 JRNL PMID 8736552 JRNL DOI 10.1016/S0969-2126(96)00059-7
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH L.TONG,G.WENGLER,M.G.ROSSMANN REMARK 1 TITL REFINED STRUCTURE OF SINDBIS VIRUS CORE PROTEIN REMARK 1 TITL 2 AND COMPARISON WITH OTHER CHYMOTRYPSIN-LIKE SERINE REMARK 1 TITL 3 PROTEINASE STRUCTURES REMARK 1 REF J.MOL.BIOL. V. 230 228 1993 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 2 REMARK 1 AUTH L.TONG,H.-K.CHOI,W.MINOR,M.G.ROSSMANN REMARK 1 TITL THE STRUCTURE DETERMINATION OF SINDBIS VIRUS CORE REMARK 1 TITL 2 PROTEIN USING ISOMORPHOUS REPLACEMENT AND REMARK 1 TITL 3 MOLECULAR REPLACEMENT AVERAGING BETWEEN TWO REMARK 1 TITL 4 CRYSTAL FORMS REMARK 1 REF ACTA CRYSTALLOGR.,SECT.A V. 48 430 1992 REMARK 1 REFN ISSN 0108-7673 REMARK 1 REFERENCE 3 REMARK 1 AUTH H.K.CHOI,L.TONG,W.MINOR,P.DUMAS,U.BOEGE, REMARK 1 AUTH 2 M.G.ROSSMANN,G.WENGLER REMARK 1 TITL STRUCTURE OF SINDBIS VIRUS CORE PROTEIN REVEALS A REMARK 1 TITL 2 CHYMOTRYPSIN-LIKE SERINE PROTEINASE AND THE REMARK 1 TITL 3 ORGANIZATION OF THE VIRION REMARK 1 REF NATURE V. 354 37 1991 REMARK 1 REFN ISSN 0028-0836
REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 5.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 15488 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2452 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 133 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.70 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1SVP COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-OCT-94 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 2.630 REMARK 200 R MERGE (I) : 0.03600 REMARK 200 R SYM (I) : NULL 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: DIMERIC 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 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 106 REMARK 465 MET B 106
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 110 100.08 -162.90 REMARK 500 ASP A 147 68.93 -69.01 REMARK 500 HIS A 184 80.58 -153.17 REMARK 500 GLU A 236 40.08 -107.24 REMARK 500 SER A 265 84.24 63.61 REMARK 500 GLU B 186 123.31 -36.32 REMARK 500 SER B 265 -93.03 -122.00 REMARK 500 REMARK 500 REMARK: NULL
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: TRI REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: SINDBIS CAPSID PROTEIN HAS THE CATALYTIC REMARK 800 TRIAD OF THE SERINE PROTEINASE. THE RESIDUES ARE SER 215, HIS REMARK 800 141, AND ASP 163 IN THE WILD-TYPE. IN THIS MUTANT STRUCTURE, REMARK 800 THE ACTIVE SITE SER 215 WAS MUTATED TO ALA TO PREVENT AUTO- REMARK 800 CATALYTIC CLEAVAGE BETWEEN TRP 264 AND SER 265.
DBREF 1SVP A 106 266 UNP P03316 POLS_SINDV 106 266 DBREF 1SVP B 106 266 UNP P03316 POLS_SINDV 106 266
SEQADV 1SVP ALA A 215 UNP P03316 SER 215 ENGINEERED SEQADV 1SVP ALA B 215 UNP P03316 SER 215 ENGINEERED
SEQRES 1 A 161 MET ALA LEU LYS LEU GLU ALA ASP ARG LEU PHE ASP VAL SEQRES 2 A 161 LYS ASN GLU ASP GLY ASP VAL ILE GLY HIS ALA LEU ALA SEQRES 3 A 161 MET GLU GLY LYS VAL MET LYS PRO LEU HIS VAL LYS GLY SEQRES 4 A 161 THR ILE ASP HIS PRO VAL LEU SER LYS LEU LYS PHE THR SEQRES 5 A 161 LYS SER SER ALA TYR ASP MET GLU PHE ALA GLN LEU PRO SEQRES 6 A 161 VAL ASN MET ARG SER GLU ALA PHE THR TYR THR SER GLU SEQRES 7 A 161 HIS PRO GLU GLY PHE TYR ASN TRP HIS HIS GLY ALA VAL SEQRES 8 A 161 GLN TYR SER GLY GLY ARG PHE THR ILE PRO ARG GLY VAL SEQRES 9 A 161 GLY GLY ARG GLY ASP ALA GLY ARG PRO ILE MET ASP ASN SEQRES 10 A 161 SER GLY ARG VAL VAL ALA ILE VAL LEU GLY GLY ALA ASP SEQRES 11 A 161 GLU GLY THR ARG THR ALA LEU SER VAL VAL THR TRP ASN SEQRES 12 A 161 SER LYS GLY LYS THR ILE LYS THR THR PRO GLU GLY THR SEQRES 13 A 161 GLU GLU TRP SER ALA SEQRES 1 B 161 MET ALA LEU LYS LEU GLU ALA ASP ARG LEU PHE ASP VAL SEQRES 2 B 161 LYS ASN GLU ASP GLY ASP VAL ILE GLY HIS ALA LEU ALA SEQRES 3 B 161 MET GLU GLY LYS VAL MET LYS PRO LEU HIS VAL LYS GLY SEQRES 4 B 161 THR ILE ASP HIS PRO VAL LEU SER LYS LEU LYS PHE THR SEQRES 5 B 161 LYS SER SER ALA TYR ASP MET GLU PHE ALA GLN LEU PRO SEQRES 6 B 161 VAL ASN MET ARG SER GLU ALA PHE THR TYR THR SER GLU SEQRES 7 B 161 HIS PRO GLU GLY PHE TYR ASN TRP HIS HIS GLY ALA VAL SEQRES 8 B 161 GLN TYR SER GLY GLY ARG PHE THR ILE PRO ARG GLY VAL SEQRES 9 B 161 GLY GLY ARG GLY ASP ALA GLY ARG PRO ILE MET ASP ASN SEQRES 10 B 161 SER GLY ARG VAL VAL ALA ILE VAL LEU GLY GLY ALA ASP SEQRES 11 B 161 GLU GLY THR ARG THR ALA LEU SER VAL VAL THR TRP ASN SEQRES 12 B 161 SER LYS GLY LYS THR ILE LYS THR THR PRO GLU GLY THR SEQRES 13 B 161 GLU GLU TRP SER ALA
FORMUL 3 HOH *133(H2 O)
HELIX 1 1 LEU A 151 LYS A 153 5 3 HELIX 2 3 VAL A 171 MET A 173 5 3 HELIX 3 4 LEU B 151 LYS B 153 5 3 HELIX 4 6 VAL B 171 MET B 173 5 3
SHEET 1 A1 6 LEU A 115 LYS A 119 0 SHEET 2 A1 6 VAL A 125 MET A 132 -1 SHEET 3 A1 6 LYS A 135 PRO A 139 -1 SHEET 4 A1 6 THR A 145 ASP A 147 -1 SHEET 5 A1 6 THR A 157 SER A 159 -1 SHEET 6 A1 6 MET A 164 GLN A 168 -1 SHEET 1 A2 8 GLY A 187 TRP A 191 0 SHEET 2 A2 8 GLY A 194 SER A 199 -1 SHEET 3 A2 8 ARG A 202 PRO A 206 -1 SHEET 4 A2 8 GLY A 216 MET A 220 -1 SHEET 5 A2 8 VAL A 226 GLU A 236 -1 SHEET 6 A2 8 ARG A 239 TRP A 247 -1 SHEET 7 A2 8 THR A 253 THR A 256 -1 SHEET 8 A2 8 THR A 261 GLU A 262 -1 SHEET 1 B1 6 LEU B 115 LYS B 119 0 SHEET 2 B1 6 VAL B 125 MET B 132 -1 SHEET 3 B1 6 LYS B 135 PRO B 139 -1 SHEET 4 B1 6 THR B 145 ASP B 147 -1 SHEET 5 B1 6 THR B 157 SER B 159 -1 SHEET 6 B1 6 MET B 164 GLN B 168 -1 SHEET 1 B2 8 GLY B 187 TRP B 191 0 SHEET 2 B2 8 GLY B 194 SER B 199 -1 SHEET 3 B2 8 ARG B 202 PRO B 206 -1 SHEET 4 B2 8 GLY B 216 MET B 220 -1 SHEET 5 B2 8 VAL B 226 GLU B 236 -1 SHEET 6 B2 8 ARG B 239 TRP B 247 -1 SHEET 7 B2 8 THR B 253 THR B 256 -1 SHEET 8 B2 8 THR B 261 GLU B 262 -1
SITE 1 TRI 6 ALA A 215 HIS A 141 ASP A 163 ALA B 215 SITE 2 TRI 6 HIS B 141 ASP B 163
CRYST1 29.000 56.500 60.830 93.10 96.73 94.93 P 1 2
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 0.034483 0.002974 0.004271 0.00000
SCALE2 0.000000 0.017765 0.001154 0.00000
SCALE3 0.000000 0.000000 0.016588 0.00000
MTRIX1 1 0.999566 0.003141 -0.029297 8.50972 1
MTRIX2 1 -0.010181 0.969880 -0.243369 25.86226 1
MTRIX3 1 0.027650 0.243561 0.969491 30.28011 1