HEADER VIRAL PROTEIN 26-JAN-00 1ECW TITLE CRYSTAL STRUCTURE OF SIMIAN IMMUNODEFICIENCY VIRUS MATRIX TITLE 2 ANTIGEN (SIV MA) AT 293K. COMPND MOL_ID: 1; COMPND 2 MOLECULE: GAG POLYPROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SIV MA; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: SIV MATRIX ANTIGEN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SIMIAN IMMUNODEFICIENCY VIRUS; SOURCE 3 ORGANISM_TAXID: 11723; SOURCE 4 STRAIN: MAC BK28; SOURCE 5 GENE: GAG; SOURCE 6 EXPRESSION_SYSTEM: UNIDENTIFIED BACULOVIRUS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 10469; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PULB5002 KEYWDS TRIMERIC ASSOCIATION, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Z.RAO,A.BELYAEV,E.FRY,P.ROY,I.M.JONES,D.I.STUART REVDAT 4 24-FEB-09 1ECW 1 VERSN REVDAT 3 02-AUG-05 1ECW 1 REMARK SCALE1 SCALE2 SCALE3 REVDAT 2 20-DEC-00 1ECW 3 REMARK DBREF ATOM REVDAT 1 16-FEB-00 1ECW 0 JRNL AUTH Z.RAO,A.S.BELYAEV,E.FRY,P.ROY,I.M.JONES,D.I.STUART JRNL TITL CRYSTAL STRUCTURE OF SIV MATRIX ANTIGEN AND JRNL TITL 2 IMPLICATIONS FOR VIRUS ASSEMBLY. JRNL REF NATURE V. 378 743 1995 JRNL REFN ISSN 0028-0836 JRNL PMID 7501025 JRNL DOI 10.1038/378743A0 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.BELYAEV,D.STUART,G.SUTTON,P.ROY REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY REMARK 1 TITL 2 INVESTIGATION OF RECOMBINANT SIMIAN REMARK 1 TITL 3 IMMUNODEFICIENCY VIRUS MATRIX ANTIGEN REMARK 1 REF J.MOL.BIOL. V. 241 744 1994 REMARK 1 REFN ISSN 0022-2836 REMARK 1 DOI 10.1006/JMBI.1994.1550 REMARK 2 REMARK 2 RESOLUTION. 2.20 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 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) (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : NULL 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) : 0.164 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 : 893 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 79 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.30 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 1ECW COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JAN-00. REMARK 100 THE RCSB ID CODE IS RCSB010457. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-94; 15-MAY-94 REMARK 200 TEMPERATURE (KELVIN) : 293.0; 293.0 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 4 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N; Y REMARK 200 RADIATION SOURCE : ROTATING ANODE; PHOTON FACTORY REMARK 200 BEAMLINE : NULL; BL-6A REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; NULL REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418; 0.97 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE; IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH; FUJI REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7686 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 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 (%) : 98.2 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.07200 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: SINGLE WAVELENGTH; NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, ISOPROPANOL, TRIS-HCL, PH REMARK 280 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 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+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 57.45000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.16877 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 10.76667 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 57.45000 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 33.16877 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 10.76667 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 57.45000 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 33.16877 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 10.76667 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 66.33755 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 21.53333 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 66.33755 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 21.53333 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 66.33755 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 21.53333 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 BIOLOGICAL ASSEMBLY MAY BE REPRESENTED BY THE REMARK 300 TRIMERIC ASSOCIATION OF MOLECULES WITHIN THE CRYSTAL. 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: TRIMERIC 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 114.90000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 57.45000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 99.50632 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 GLY A 2 REMARK 465 ALA A 3 REMARK 465 ARG A 4 REMARK 465 ASN A 5 REMARK 465 LYS A 120 REMARK 465 THR A 121 REMARK 465 SER A 122 REMARK 465 ARG A 123 REMARK 465 PRO A 124 REMARK 465 THR A 125 REMARK 465 ALA A 126 REMARK 465 PRO A 127 REMARK 465 SER A 128 REMARK 465 SER A 129 REMARK 465 GLY A 130 REMARK 465 ARG A 131 REMARK 465 GLY A 132 REMARK 465 GLY A 133 REMARK 465 ASN A 134 REMARK 465 TYR A 135 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 VAL A 7 -78.22 66.22 REMARK 500 SER A 9 -175.84 -60.13 REMARK 500 THR A 114 32.71 -89.42 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 IPA A 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ED1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SIMIAN IMMUNODEFICIENCY VIRUS MATRIX REMARK 900 ANTIGEN (SIV MA) AT 100K. DBREF 1ECW A 1 135 UNP Q88000 Q88000_SIVCZ 1 135 SEQRES 1 A 135 MET GLY ALA ARG ASN SER VAL LEU SER GLY LYS LYS ALA SEQRES 2 A 135 ASP GLU LEU GLU LYS ILE ARG LEU ARG PRO GLY GLY LYS SEQRES 3 A 135 LYS LYS TYR MET LEU LYS HIS VAL VAL TRP ALA ALA ASN SEQRES 4 A 135 GLU LEU ASP ARG PHE GLY LEU ALA GLU SER LEU LEU GLU SEQRES 5 A 135 ASN LYS GLU GLY CYS GLN LYS ILE LEU SER VAL LEU ALA SEQRES 6 A 135 PRO LEU VAL PRO THR GLY SER GLU ASN LEU LYS SER LEU SEQRES 7 A 135 TYR ASN THR VAL CYS VAL ILE TRP CYS ILE HIS ALA GLU SEQRES 8 A 135 GLU LYS VAL LYS HIS THR GLU GLU ALA LYS GLN ILE VAL SEQRES 9 A 135 GLN ARG HIS LEU VAL VAL GLU THR GLY THR ALA GLU THR SEQRES 10 A 135 MET PRO LYS THR SER ARG PRO THR ALA PRO SER SER GLY SEQRES 11 A 135 ARG GLY GLY ASN TYR HET IPA A 501 4 HETNAM IPA ISOPROPYL ALCOHOL HETSYN IPA 2-PROPANOL FORMUL 2 IPA C3 H8 O FORMUL 3 HOH *75(H2 O) HELIX 1 1 SER A 9 GLU A 17 1 9 HELIX 2 2 MET A 30 PHE A 44 1 15 HELIX 3 3 ALA A 47 GLU A 52 5 6 HELIX 4 4 ASN A 53 ALA A 65 1 13 HELIX 5 5 PRO A 66 GLY A 71 5 6 HELIX 6 6 SER A 72 ALA A 90 1 19 HELIX 7 7 HIS A 96 VAL A 109 1 14 SHEET 1 A 2 VAL A 110 GLU A 111 0 SHEET 2 A 2 GLU A 116 THR A 117 -1 O THR A 117 N VAL A 110 SITE 1 AC1 6 PHE A 44 GLY A 45 LEU A 46 LEU A 67 SITE 2 AC1 6 THR A 70 GLY A 71 CRYST1 114.900 114.900 32.300 90.00 90.00 120.00 H 3 9 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 0.008703 0.005025 0.000000 0.00000 SCALE2 0.000000 0.010050 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030960 0.00000 MASTER 294 0 1 7 2 0 2 6 0 0 0 11 END