HEADER VIRAL PROTEIN 10-DEC-12 4ICA TITLE CRYSTAL STRUCTURE OF A C-TERMINAL TRUNCATED FORM OF THE MATRIX SUBUNIT TITLE 2 (P15) OF FELINE IMMUNODEFICIENCY VIRUS (FIV) COMPND MOL_ID: 1; COMPND 2 MOLECULE: MATRIX PROTEIN P15; COMPND 3 CHAIN: A, B; 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 03-APR-24 4ICA 1 REMARK REVDAT 2 28-FEB-24 4ICA 1 REMARK SEQADV REVDAT 1 10-JUL-13 4ICA 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. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.1_1168) 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 6138 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 306 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 19.6763 - 3.3986 0.98 2939 155 0.2003 0.2694 REMARK 3 2 3.3986 - 2.7000 0.98 2893 151 0.2348 0.3002 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) : 0.400 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.140 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 : 0.002 1868 REMARK 3 ANGLE : 0.417 2488 REMARK 3 CHIRALITY : 0.028 270 REMARK 3 PLANARITY : 0.002 320 REMARK 3 DIHEDRAL : 12.759 730 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 4ICA 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_1000076573. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-OCT-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97239 REMARK 200 MONOCHROMATOR : CYLINDRICAL GRAZING INCIDENCE REMARK 200 MIRROR + CHANNEL-CUT CRYO-COOLED REMARK 200 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 : 6139 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 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 (%) : 98.1 REMARK 200 DATA REDUNDANCY : 3.300 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) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.77 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8 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 : 4.800 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: FULL-LENGTH FIV P15 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL, 25% (W/V) POLYETHYLENE REMARK 280 GLYCOL 6000, PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 35.65000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 1 REMARK 465 LEU A 121 REMARK 465 VAL A 122 REMARK 465 PRO A 123 REMARK 465 ARG A 124 REMARK 465 GLY A 125 REMARK 465 SER A 126 REMARK 465 LEU A 127 REMARK 465 GLU A 128 REMARK 465 HIS A 129 REMARK 465 HIS A 130 REMARK 465 HIS A 131 REMARK 465 HIS A 132 REMARK 465 HIS A 133 REMARK 465 HIS A 134 REMARK 465 MET B 1 REMARK 465 LEU B 121 REMARK 465 VAL B 122 REMARK 465 PRO B 123 REMARK 465 ARG B 124 REMARK 465 GLY B 125 REMARK 465 SER B 126 REMARK 465 LEU B 127 REMARK 465 GLU B 128 REMARK 465 HIS B 129 REMARK 465 HIS B 130 REMARK 465 HIS B 131 REMARK 465 HIS B 132 REMARK 465 HIS B 133 REMARK 465 HIS B 134 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 ASN A 3 87.95 -155.27 REMARK 500 LYS A 26 56.22 -99.95 REMARK 500 GLN B 5 55.18 -170.02 REMARK 500 LYS B 26 45.23 -99.28 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 7PE A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 7PE B 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4IC9 RELATED DB: PDB DBREF 4ICA A 1 120 UNP P16087 GAG_FIVPE 1 120 DBREF 4ICA B 1 120 UNP P16087 GAG_FIVPE 1 120 SEQADV 4ICA LEU A 121 UNP P16087 EXPRESSION TAG SEQADV 4ICA VAL A 122 UNP P16087 EXPRESSION TAG SEQADV 4ICA PRO A 123 UNP P16087 EXPRESSION TAG SEQADV 4ICA ARG A 124 UNP P16087 EXPRESSION TAG SEQADV 4ICA GLY A 125 UNP P16087 EXPRESSION TAG SEQADV 4ICA SER A 126 UNP P16087 EXPRESSION TAG SEQADV 4ICA LEU A 127 UNP P16087 EXPRESSION TAG SEQADV 4ICA GLU A 128 UNP P16087 EXPRESSION TAG SEQADV 4ICA HIS A 129 UNP P16087 EXPRESSION TAG SEQADV 4ICA HIS A 130 UNP P16087 EXPRESSION TAG SEQADV 4ICA HIS A 131 UNP P16087 EXPRESSION TAG SEQADV 4ICA HIS A 132 UNP P16087 EXPRESSION TAG SEQADV 4ICA HIS A 133 UNP P16087 EXPRESSION TAG SEQADV 4ICA HIS A 134 UNP P16087 EXPRESSION TAG SEQADV 4ICA LEU B 121 UNP P16087 EXPRESSION TAG SEQADV 4ICA VAL B 122 UNP P16087 EXPRESSION TAG SEQADV 4ICA PRO B 123 UNP P16087 EXPRESSION TAG SEQADV 4ICA ARG B 124 UNP P16087 EXPRESSION TAG SEQADV 4ICA GLY B 125 UNP P16087 EXPRESSION TAG SEQADV 4ICA SER B 126 UNP P16087 EXPRESSION TAG SEQADV 4ICA LEU B 127 UNP P16087 EXPRESSION TAG SEQADV 4ICA GLU B 128 UNP P16087 EXPRESSION TAG SEQADV 4ICA HIS B 129 UNP P16087 EXPRESSION TAG SEQADV 4ICA HIS B 130 UNP P16087 EXPRESSION TAG SEQADV 4ICA HIS B 131 UNP P16087 EXPRESSION TAG SEQADV 4ICA HIS B 132 UNP P16087 EXPRESSION TAG SEQADV 4ICA HIS B 133 UNP P16087 EXPRESSION TAG SEQADV 4ICA HIS B 134 UNP P16087 EXPRESSION TAG SEQRES 1 A 134 MET GLY ASN GLY GLN GLY ARG ASP TRP LYS MET ALA ILE SEQRES 2 A 134 LYS ARG CYS SER ASN VAL ALA VAL GLY VAL GLY GLY LYS SEQRES 3 A 134 SER LYS LYS PHE GLY GLU GLY ASN PHE ARG TRP ALA ILE SEQRES 4 A 134 ARG MET ALA ASN VAL SER THR GLY ARG GLU PRO GLY ASP SEQRES 5 A 134 ILE PRO GLU THR LEU ASP GLN LEU ARG LEU VAL ILE CYS SEQRES 6 A 134 ASP LEU GLN GLU ARG ARG GLU LYS PHE GLY SER SER LYS SEQRES 7 A 134 GLU ILE ASP MET ALA ILE VAL THR LEU LYS VAL PHE ALA SEQRES 8 A 134 VAL ALA GLY LEU LEU ASN MET THR VAL SER THR ALA ALA SEQRES 9 A 134 ALA ALA GLU ASN MET TYR SER GLN MET GLY LEU ASP THR SEQRES 10 A 134 ARG PRO SER LEU VAL PRO ARG GLY SER LEU GLU HIS HIS SEQRES 11 A 134 HIS HIS HIS HIS SEQRES 1 B 134 MET GLY ASN GLY GLN GLY ARG ASP TRP LYS MET ALA ILE SEQRES 2 B 134 LYS ARG CYS SER ASN VAL ALA VAL GLY VAL GLY GLY LYS SEQRES 3 B 134 SER LYS LYS PHE GLY GLU GLY ASN PHE ARG TRP ALA ILE SEQRES 4 B 134 ARG MET ALA ASN VAL SER THR GLY ARG GLU PRO GLY ASP SEQRES 5 B 134 ILE PRO GLU THR LEU ASP GLN LEU ARG LEU VAL ILE CYS SEQRES 6 B 134 ASP LEU GLN GLU ARG ARG GLU LYS PHE GLY SER SER LYS SEQRES 7 B 134 GLU ILE ASP MET ALA ILE VAL THR LEU LYS VAL PHE ALA SEQRES 8 B 134 VAL ALA GLY LEU LEU ASN MET THR VAL SER THR ALA ALA SEQRES 9 B 134 ALA ALA GLU ASN MET TYR SER GLN MET GLY LEU ASP THR SEQRES 10 B 134 ARG PRO SER LEU VAL PRO ARG GLY SER LEU GLU HIS HIS SEQRES 11 B 134 HIS HIS HIS HIS HET 7PE A 201 21 HET 7PE B 201 21 HETNAM 7PE 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY) HETNAM 2 7PE ETHOXY)ETHANOL HETSYN 7PE POLYETHYLENE GLYCOL FRAGMENT FORMUL 3 7PE 2(C14 H30 O7) FORMUL 5 HOH *23(H2 O) HELIX 1 1 GLY A 6 CYS A 16 1 11 HELIX 2 2 SER A 17 VAL A 19 5 3 HELIX 3 3 GLY A 31 THR A 46 1 16 HELIX 4 4 THR A 56 GLY A 75 1 20 HELIX 5 5 SER A 77 ALA A 93 1 17 HELIX 6 6 THR A 102 MET A 113 1 12 HELIX 7 7 GLY B 6 CYS B 16 1 11 HELIX 8 8 SER B 17 VAL B 19 5 3 HELIX 9 9 GLY B 31 THR B 46 1 16 HELIX 10 10 THR B 56 GLY B 75 1 20 HELIX 11 11 SER B 77 ALA B 93 1 17 HELIX 12 12 THR B 102 MET B 113 1 12 SITE 1 AC1 6 GLY A 33 ASN A 34 ARG A 36 ARG A 40 SITE 2 AC1 6 ASN A 97 THR A 99 SITE 1 AC2 8 GLY B 33 ASN B 34 ARG B 36 TRP B 37 SITE 2 AC2 8 ARG B 40 MET B 82 ASN B 97 THR B 99 CRYST1 28.480 71.300 57.060 90.00 99.63 90.00 P 1 21 1 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 0.035112 0.000000 0.005959 0.00000 SCALE2 0.000000 0.014025 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017776 0.00000