HEADER VIRAL PROTEIN 10-DEC-12 4IC9 TITLE CRYSTAL STRUCTURE OF THE FULL-LENGTH MATRIX SUBUNIT (P15) OF THE TITLE 2 FELINE IMMUNODEFICIENCY VIRUS (FIV) GAG POLYPROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: MATRIX PROTEIN P15; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: FELINE IMMUNODEFICIENCY VIRUS; SOURCE 3 ORGANISM_COMMON: FIV; SOURCE 4 ORGANISM_TAXID: 11674; SOURCE 5 STRAIN: PETALUMA; SOURCE 6 GENE: FIV GAG, GAG; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21-GOLD(DE3)PLYSS AG; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PRSET-B KEYWDS FIV, P15, RETROVIRAL MATRIX PROTEIN, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.SERRIERE,X.ROBERT,M.PEREZ,P.GOUET,C.GUILLON REVDAT 3 20-SEP-23 4IC9 1 REMARK SEQADV REVDAT 2 15-NOV-17 4IC9 1 REMARK REVDAT 1 10-JUL-13 4IC9 0 JRNL AUTH J.SERRIERE,X.ROBERT,M.PEREZ,P.GOUET,C.GUILLON JRNL TITL BIOPHYSICAL CHARACTERIZATION AND CRYSTAL STRUCTURE OF THE JRNL TITL 2 FELINE IMMUNODEFICIENCY VIRUS P15 MATRIX PROTEIN. JRNL REF RETROVIROLOGY V. 10 64 2013 JRNL REFN ESSN 1742-4690 JRNL PMID 23800358 JRNL DOI 10.1186/1742-4690-10-64 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8_1069) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.31 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.010 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 7646 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 383 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 19.3110 - 2.8822 1.00 2520 133 0.1874 0.2538 REMARK 3 2 2.8822 - 2.2889 1.00 2386 126 0.2111 0.2664 REMARK 3 3 2.2889 - 2.0000 1.00 2357 124 0.1695 0.2406 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.850 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 1009 REMARK 3 ANGLE : 1.005 1343 REMARK 3 CHIRALITY : 0.067 144 REMARK 3 PLANARITY : 0.005 176 REMARK 3 DIHEDRAL : 14.124 389 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4IC9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JAN-13. REMARK 100 THE DEPOSITION ID IS D_1000076572. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-FEB-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98011 REMARK 200 MONOCHROMATOR : KIRKPATRICK-BAEZ PAIR OF BI REMARK 200 -MORPH MIRRORS + CHANNEL-CUT REMARK 200 CRYO-COOLED SILICON MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7647 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : NULL 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) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 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 : 4.780 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MRBUMP REMARK 200 STARTING MODEL: PDB ENTRY 1ECW, SIV MATRIX PROTEIN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE, 25% (W/V) REMARK 280 POLYETHYLENE GLYCOL 3,000, PH 6.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-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 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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 26.50500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.60000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.50500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.60000 REMARK 290 SMTRY3 4 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 1 REMARK 465 GLY A 2 REMARK 465 ASN A 3 REMARK 465 ALA A 134 REMARK 465 TYR A 135 REMARK 465 LEU A 136 REMARK 465 VAL A 137 REMARK 465 PRO A 138 REMARK 465 ARG A 139 REMARK 465 GLY A 140 REMARK 465 SER A 141 REMARK 465 LEU A 142 REMARK 465 GLU A 143 REMARK 465 HIS A 144 REMARK 465 HIS A 145 REMARK 465 HIS A 146 REMARK 465 HIS A 147 REMARK 465 HIS A 148 REMARK 465 HIS A 149 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 GLN A 5 -11.08 -143.85 REMARK 500 VAL A 23 28.10 -71.28 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 EDO A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 204 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4ICA RELATED DB: PDB DBREF 4IC9 A 1 135 UNP P16087 GAG_FIVPE 1 135 SEQADV 4IC9 LEU A 136 UNP P16087 EXPRESSION TAG SEQADV 4IC9 VAL A 137 UNP P16087 EXPRESSION TAG SEQADV 4IC9 PRO A 138 UNP P16087 EXPRESSION TAG SEQADV 4IC9 ARG A 139 UNP P16087 EXPRESSION TAG SEQADV 4IC9 GLY A 140 UNP P16087 EXPRESSION TAG SEQADV 4IC9 SER A 141 UNP P16087 EXPRESSION TAG SEQADV 4IC9 LEU A 142 UNP P16087 EXPRESSION TAG SEQADV 4IC9 GLU A 143 UNP P16087 EXPRESSION TAG SEQADV 4IC9 HIS A 144 UNP P16087 EXPRESSION TAG SEQADV 4IC9 HIS A 145 UNP P16087 EXPRESSION TAG SEQADV 4IC9 HIS A 146 UNP P16087 EXPRESSION TAG SEQADV 4IC9 HIS A 147 UNP P16087 EXPRESSION TAG SEQADV 4IC9 HIS A 148 UNP P16087 EXPRESSION TAG SEQADV 4IC9 HIS A 149 UNP P16087 EXPRESSION TAG SEQRES 1 A 149 MET GLY ASN GLY GLN GLY ARG ASP TRP LYS MET ALA ILE SEQRES 2 A 149 LYS ARG CYS SER ASN VAL ALA VAL GLY VAL GLY GLY LYS SEQRES 3 A 149 SER LYS LYS PHE GLY GLU GLY ASN PHE ARG TRP ALA ILE SEQRES 4 A 149 ARG MET ALA ASN VAL SER THR GLY ARG GLU PRO GLY ASP SEQRES 5 A 149 ILE PRO GLU THR LEU ASP GLN LEU ARG LEU VAL ILE CYS SEQRES 6 A 149 ASP LEU GLN GLU ARG ARG GLU LYS PHE GLY SER SER LYS SEQRES 7 A 149 GLU ILE ASP MET ALA ILE VAL THR LEU LYS VAL PHE ALA SEQRES 8 A 149 VAL ALA GLY LEU LEU ASN MET THR VAL SER THR ALA ALA SEQRES 9 A 149 ALA ALA GLU ASN MET TYR SER GLN MET GLY LEU ASP THR SEQRES 10 A 149 ARG PRO SER MET LYS GLU ALA GLY GLY LYS GLU GLU GLY SEQRES 11 A 149 PRO PRO GLN ALA TYR LEU VAL PRO ARG GLY SER LEU GLU SEQRES 12 A 149 HIS HIS HIS HIS HIS HIS HET EDO A 201 4 HET EDO A 202 4 HET EDO A 203 4 HET EDO A 204 4 HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO 4(C2 H6 O2) FORMUL 6 HOH *28(H2 O) HELIX 1 1 GLY A 6 SER A 17 1 12 HELIX 2 2 GLY A 31 THR A 46 1 16 HELIX 3 3 THR A 56 GLY A 75 1 20 HELIX 4 4 SER A 77 GLY A 94 1 18 HELIX 5 5 THR A 102 MET A 113 1 12 HELIX 6 6 SER A 120 GLY A 125 1 6 CISPEP 1 GLY A 24 GLY A 25 0 3.71 SITE 1 AC1 6 ARG A 70 GLY A 75 SER A 77 ILE A 80 SITE 2 AC1 6 GLN A 112 HOH A 307 SITE 1 AC2 4 MET A 11 LYS A 73 LYS A 122 GLU A 123 SITE 1 AC3 5 GLN A 68 ARG A 71 ILE A 84 GLU A 107 SITE 2 AC3 5 HOH A 306 SITE 1 AC4 5 ASP A 8 ILE A 53 PRO A 54 GLU A 55 SITE 2 AC4 5 LEU A 95 CRYST1 53.010 71.200 28.190 90.00 90.00 90.00 P 21 21 2 4 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 0.018864 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014045 0.000000 0.00000 SCALE3 0.000000 0.000000 0.035474 0.00000