HEADER VIRAL PROTEIN 05-MAY-96 1KXD TITLE SINDBIS VIRUS CAPSID (N222L MUTANT), TETRAGONAL CRYSTAL FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: SINDBIS VIRUS CAPSID PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: MET 106 - ALA 264 OF THE NATIVE SINDBIS CAPSID; COMPND 5 EC: 3.4.21.-; COMPND 6 ENGINEERED: YES; COMPND 7 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 PROTEINASE, KEYWDS 2 WILD TYPE, COAT PROTEIN, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.-K.CHOI,M.G.ROSSMANN REVDAT 5 14-FEB-24 1KXD 1 REMARK REVDAT 4 03-NOV-21 1KXD 1 SEQADV REVDAT 3 24-FEB-09 1KXD 1 VERSN REVDAT 2 01-APR-03 1KXD 1 JRNL REVDAT 1 08-NOV-96 1KXD 0 JRNL AUTH H.K.CHOI,S.LEE,Y.P.ZHANG,B.R.MCKINNEY,G.WENGLER, JRNL AUTH 2 M.G.ROSSMANN,R.J.KUHN JRNL TITL STRUCTURAL ANALYSIS OF SINDBIS VIRUS CAPSID MUTANTS JRNL TITL 2 INVOLVING ASSEMBLY AND CATALYSIS. JRNL REF J.MOL.BIOL. V. 262 151 1996 JRNL REFN ISSN 0022-2836 JRNL PMID 8831786 JRNL DOI 10.1006/JMBI.1996.0505 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 AND REMARK 1 TITL 2 COMPARISON WITH OTHER CHYMOTRYPSIN-LIKE SERINE PROTEINASE REMARK 1 TITL 3 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 PROTEIN REMARK 1 TITL 2 USING ISOMORPHOUS REPLACEMENT AND MOLECULAR REPLACEMENT REMARK 1 TITL 3 AVERAGING BETWEEN TWO 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,M.G.ROSSMANN, REMARK 1 AUTH 2 G.WENGLER REMARK 1 TITL STRUCTURE OF SINDBIS VIRUS CORE PROTEIN REVEALS A REMARK 1 TITL 2 CHYMOTRYPSIN-LIKE SERINE PROTEINASE AND THE ORGANIZATION OF REMARK 1 TITL 3 THE VIRION REMARK 1 REF NATURE V. 354 37 1991 REMARK 1 REFN ISSN 0028-0836 REMARK 2 REMARK 2 RESOLUTION. 3.00 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 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 : 3102 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) : 0.179 REMARK 3 FREE R VALUE : NULL 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 : 1216 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.70 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) : NULL 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) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.600 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 1KXD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000174518. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-DEC-93 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 : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SIEMENS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4040 REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 85.7 REMARK 200 DATA REDUNDANCY : 2.920 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 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 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 (%): 53.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 -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 54.90000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 28.50000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 28.50000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 82.35000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 28.50000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 28.50000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 27.45000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 28.50000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.50000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 82.35000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 28.50000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.50000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 27.45000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 54.90000 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 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 ASP A 147 72.72 -69.43 REMARK 500 HIS A 148 118.87 -160.75 REMARK 500 VAL A 171 -46.73 -29.45 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 TRIAD REMARK 800 OF THE SERINE PROTEINASE. THE RESIDUES ARE SER 215, HIS 141, AND REMARK 800 ASP 163. DBREF 1KXD A 106 264 UNP P03316 POLS_SINDV 106 264 SEQADV 1KXD LEU A 222 UNP P03316 ASN 222 ENGINEERED MUTATION SEQRES 1 A 159 MET ALA LEU LYS LEU GLU ALA ASP ARG LEU PHE ASP VAL SEQRES 2 A 159 LYS ASN GLU ASP GLY ASP VAL ILE GLY HIS ALA LEU ALA SEQRES 3 A 159 MET GLU GLY LYS VAL MET LYS PRO LEU HIS VAL LYS GLY SEQRES 4 A 159 THR ILE ASP HIS PRO VAL LEU SER LYS LEU LYS PHE THR SEQRES 5 A 159 LYS SER SER ALA TYR ASP MET GLU PHE ALA GLN LEU PRO SEQRES 6 A 159 VAL ASN MET ARG SER GLU ALA PHE THR TYR THR SER GLU SEQRES 7 A 159 HIS PRO GLU GLY PHE TYR ASN TRP HIS HIS GLY ALA VAL SEQRES 8 A 159 GLN TYR SER GLY GLY ARG PHE THR ILE PRO ARG GLY VAL SEQRES 9 A 159 GLY GLY ARG GLY ASP SER GLY ARG PRO ILE MET ASP LEU SEQRES 10 A 159 SER GLY ARG VAL VAL ALA ILE VAL LEU GLY GLY ALA ASP SEQRES 11 A 159 GLU GLY THR ARG THR ALA LEU SER VAL VAL THR TRP ASN SEQRES 12 A 159 SER LYS GLY LYS THR ILE LYS THR THR PRO GLU GLY THR SEQRES 13 A 159 GLU GLU TRP HELIX 1 1 LEU A 151 LYS A 153 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 ILE A 146 -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 PRO A 218 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 GLU A 262 GLU A 263 -1 SITE 1 TRI 3 SER A 215 HIS A 141 ASP A 163 CRYST1 57.000 57.000 109.800 90.00 90.00 90.00 P 43 21 2 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 0.017544 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017544 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009107 0.00000