HEADER VIRAL PROTEIN 29-OCT-08 3F2E TITLE CRYSTAL STRUCTURE OF YELLOWSTONE SIRV COAT PROTEIN C-TERMINUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: SIRV COAT PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SULFOLOBUS ISLANDICUS RUDIVIRUS 1 VARIANT YNP; SOURCE 3 ORGANISM_TAXID: 187213; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET31A KEYWDS FOUR HELIX BUNDLE, VIRUS COAT PROTEIN, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.E.TAUROG,B.R.SZYMCZYNA,J.R.WILLIAMSON,J.E.JOHNSON REVDAT 5 03-APR-24 3F2E 1 REMARK REVDAT 4 27-DEC-23 3F2E 1 REMARK REVDAT 3 26-FEB-20 3F2E 1 REMARK REVDAT 2 21-MAR-12 3F2E 1 JRNL VERSN SOURCE REVDAT 1 21-APR-09 3F2E 0 JRNL AUTH B.R.SZYMCZYNA,R.E.TAUROG,M.J.YOUNG,J.C.SNYDER,J.E.JOHNSON, JRNL AUTH 2 J.R.WILLIAMSON JRNL TITL SYNERGY OF NMR, COMPUTATION, AND X-RAY CRYSTALLOGRAPHY FOR JRNL TITL 2 STRUCTURAL BIOLOGY. JRNL REF STRUCTURE V. 17 499 2009 JRNL REFN ISSN 0969-2126 JRNL PMID 19368883 JRNL DOI 10.1016/J.STR.2009.03.001 REMARK 2 REMARK 2 RESOLUTION. 1.67 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 1.67 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 14055 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 703 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 31.6474 - 2.8522 1.00 2840 149 0.1870 0.2184 REMARK 3 2 2.8522 - 2.2641 1.00 2691 142 0.1792 0.1771 REMARK 3 3 2.2641 - 1.9779 1.00 2657 140 0.1639 0.1778 REMARK 3 4 1.9779 - 1.7971 0.99 2623 138 0.1753 0.1954 REMARK 3 5 1.7971 - 1.6680 0.97 2541 134 0.1830 0.2313 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 : 0.39 REMARK 3 B_SOL : 49.57 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.68 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.25830 REMARK 3 B22 (A**2) : -0.25830 REMARK 3 B33 (A**2) : -5.77400 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 : 0.005 NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : 15.532 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 3F2E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-OCT-08. REMARK 100 THE DEPOSITION ID IS D_1000050060. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-AUG-08 REMARK 200 TEMPERATURE (KELVIN) : 173 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-D REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.542 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14062 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.668 REMARK 200 RESOLUTION RANGE LOW (A) : 44.588 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 16.80 REMARK 200 R MERGE (I) : 0.03400 REMARK 200 R SYM (I) : 0.06200 REMARK 200 FOR THE DATA SET : 33.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.67 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.6 REMARK 200 DATA REDUNDANCY IN SHELL : 14.50 REMARK 200 R MERGE FOR SHELL (I) : 0.20300 REMARK 200 R SYM FOR SHELL (I) : 0.37100 REMARK 200 FOR SHELL : 8.270 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: CS-ROSETTA MODEL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SIRV CP (RESIDUES 46-134) AT 19 OR 30 REMARK 280 MG/ML IN 20 MM NA MES PH 6.0 WAS MIXED 1:1 WITH 25% PEG 20,000, REMARK 280 0.1 M NA CITRATE PH 3.6, 4-9% SUCROSE. CRYSTALS WERE FROZEN IN REMARK 280 OF 14% PEG 20,000, 50 MM SODIUM CITRATE PH 3.6, 15-25% SUCROSE, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 299K 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 38.89500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 27.20500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 27.20500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 58.34250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 27.20500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 27.20500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 19.44750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 27.20500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 27.20500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 58.34250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 27.20500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 27.20500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 19.44750 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 38.89500 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 45 REMARK 465 GLN A 46 REMARK 465 THR A 47 REMARK 465 ASN A 48 REMARK 465 VAL A 49 REMARK 465 PRO A 50 REMARK 465 LYS A 51 REMARK 465 GLY A 135 REMARK 465 GLY A 136 REMARK 465 SER A 137 REMARK 465 GLY A 138 REMARK 465 HIS A 139 REMARK 465 HIS A 140 REMARK 465 HIS A 141 REMARK 465 HIS A 142 REMARK 465 HIS A 143 REMARK 465 HIS A 144 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 PHE A 52 CB CG CD1 CD2 CE1 CE2 CZ REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CIT A 200 DBREF 3F2E A 45 144 PDB 3F2E 3F2E 45 144 SEQRES 1 A 100 MET GLN THR ASN VAL PRO LYS PHE THR ALA VAL ALA GLU SEQRES 2 A 100 GLN VAL SER ALA VAL LEU SER GLN TYR GLY ILE THR GLY SEQRES 3 A 100 PRO ASN ARG ALA ILE TYR GLN GLY PHE GLY LEU LYS VAL SEQRES 4 A 100 ALA ARG ALA LEU ASN ARG LEU GLY GLY GLY PRO ALA LEU SEQRES 5 A 100 VAL ASN MET ILE ASN GLY LEU LYS ALA TYR TYR ILE SER SEQRES 6 A 100 ALA PHE ASN ALA ASN PRO THR VAL LEU ASP ALA VAL THR SEQRES 7 A 100 ASP ILE ILE THR GLY SER PRO THR GLY TYR VAL SER GLY SEQRES 8 A 100 GLY SER GLY HIS HIS HIS HIS HIS HIS HET CIT A 200 13 HETNAM CIT CITRIC ACID FORMUL 2 CIT C6 H8 O7 FORMUL 3 HOH *80(H2 O) HELIX 1 1 THR A 53 TYR A 66 1 14 HELIX 2 2 ASN A 72 LEU A 90 1 19 HELIX 3 3 PRO A 94 PHE A 111 1 18 HELIX 4 4 PRO A 115 THR A 126 1 12 SITE 1 AC1 6 LYS A 82 ARG A 85 ALA A 86 TYR A 106 SITE 2 AC1 6 TYR A 107 PHE A 111 CRYST1 54.410 54.410 77.790 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 0.018379 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018379 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012855 0.00000