HEADER VIRAL PROTEIN 02-NOV-12 4HTW TITLE SIVMAC239 CAPSID N-TERMINAL DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: GAG PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN, UNP RESIDUES 3-145; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SIMIAN IMMUNODEFICIENCY VIRUS; SOURCE 3 ORGANISM_COMMON: SIV; SOURCE 4 ORGANISM_TAXID: 11723; SOURCE 5 GENE: SYNTHETIC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET303 KEYWDS SIV CAPSID PROTEIN, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.G.SCHMIDT REVDAT 4 28-FEB-24 4HTW 1 REMARK REVDAT 3 15-NOV-17 4HTW 1 REMARK REVDAT 2 19-JUN-13 4HTW 1 JRNL REVDAT 1 22-MAY-13 4HTW 0 JRNL AUTH K.R.MCCARTHY,A.G.SCHMIDT,A.KIRMAIER,A.L.WYAND,R.M.NEWMAN, JRNL AUTH 2 W.E.JOHNSON JRNL TITL GAIN-OF-SENSITIVITY MUTATIONS IN A TRIM5-RESISTANT PRIMARY JRNL TITL 2 ISOLATE OF PATHOGENIC SIV IDENTIFY TWO INDEPENDENT CONSERVED JRNL TITL 3 DETERMINANTS OF TRIM5ALPHA SPECIFICITY. JRNL REF PLOS PATHOG. V. 9 03352 2013 JRNL REFN ISSN 1553-7366 JRNL PMID 23675300 JRNL DOI 10.1371/JOURNAL.PPAT.1003352 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.3_928 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.27 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 3497 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.256 REMARK 3 R VALUE (WORKING SET) : 0.254 REMARK 3 FREE R VALUE : 0.293 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.350 REMARK 3 FREE R VALUE TEST SET COUNT : 152 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.73 REMARK 3 K_SOL : 0.30 REMARK 3 B_SOL : 69.57 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 38.150 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 109.2 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -10.61850 REMARK 3 B22 (A**2) : 42.63820 REMARK 3 B33 (A**2) : -32.01970 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 4HTW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-NOV-12. REMARK 100 THE DEPOSITION ID IS D_1000075914. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-MAR-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3537 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.36500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG 2000 MME, 10MM NICKEL CHLORIDE REMARK 280 AND 100MM TRIS., PH 8.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 12.30700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.28300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.33150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.28300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.30700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.33150 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 PRO A 88 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O ILE A 26 N LYS A 30 1.99 REMARK 500 REMARK 500 REMARK: NULL 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 ILE A 26 -74.90 -72.48 REMARK 500 LYS A 30 73.24 49.35 REMARK 500 PHE A 31 -121.87 51.88 REMARK 500 ALA A 33 -50.41 -125.26 REMARK 500 GLU A 34 -5.31 -50.64 REMARK 500 VAL A 58 32.94 -142.24 REMARK 500 ALA A 63 0.25 -66.45 REMARK 500 LEU A 81 -71.00 -102.52 REMARK 500 GLN A 90 133.41 66.21 REMARK 500 ASN A 120 72.29 64.52 REMARK 500 ILE A 127 -64.82 -99.59 REMARK 500 REMARK 500 REMARK: NULL DBREF 4HTW A 1 143 UNP Q8Q5M0 Q8Q5M0_SIV 3 145 SEQRES 1 A 143 PRO VAL GLN GLN ILE GLY GLY ASN TYR VAL HIS LEU PRO SEQRES 2 A 143 LEU SER PRO ARG THR LEU ASN ALA TRP VAL LYS LEU ILE SEQRES 3 A 143 GLU GLU LYS LYS PHE GLY ALA GLU VAL VAL PRO GLY PHE SEQRES 4 A 143 GLN ALA LEU SER GLU GLY CYS THR PRO TYR ASP ILE ASN SEQRES 5 A 143 GLN MET LEU ASN CYS VAL GLY ASP HIS GLN ALA ALA MET SEQRES 6 A 143 GLN ILE ILE ARG ASP ILE ILE ASN GLU GLU ALA ALA ASP SEQRES 7 A 143 TRP ASP LEU GLN HIS PRO GLN PRO ALA PRO GLN GLN GLY SEQRES 8 A 143 GLN LEU ARG GLU PRO SER GLY SER ASP ILE ALA GLY THR SEQRES 9 A 143 THR SER SER VAL ASP GLU GLN ILE GLN TRP MET TYR ARG SEQRES 10 A 143 GLN GLN ASN PRO ILE PRO VAL GLY ASN ILE TYR ARG ARG SEQRES 11 A 143 TRP ILE GLN LEU GLY LEU GLN LYS CYS VAL ARG MET TYR HELIX 1 1 SER A 15 LYS A 30 1 16 HELIX 2 2 GLU A 34 GLU A 44 1 11 HELIX 3 3 THR A 47 CYS A 57 1 11 HELIX 4 4 ALA A 64 HIS A 83 1 20 HELIX 5 5 SER A 97 ALA A 102 1 6 HELIX 6 6 SER A 107 TYR A 116 1 10 HELIX 7 7 VAL A 124 MET A 142 1 19 SHEET 1 A 2 VAL A 2 ILE A 5 0 SHEET 2 A 2 ASN A 8 HIS A 11 -1 O ASN A 8 N ILE A 5 CISPEP 1 GLN A 85 PRO A 86 0 -20.43 CRYST1 24.614 56.663 102.566 90.00 90.00 90.00 P 21 21 21 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 0.040627 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017648 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009750 0.00000