HEADER VIRAL PROTEIN 12-AUG-14 4R2H TITLE THE CRYSTAL STRUCTURE OF B204, THE DNA-PACKAGING ATPASE FROM TITLE 2 SULFOLOBUS TURRETED ICOSAHEDRAL VIRUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: STIV B204 ATPASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SULFOLOBUS TURRETED ICOSAHEDRAL VIRUS 1; SOURCE 3 ORGANISM_TAXID: 269145; SOURCE 4 GENE: B164, B204; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ROSETTA(DE3)PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PDEST14 KEYWDS WALKER A MOTIF, WALKER B MOTIF, ARGININE FINGER, P-LOOP ATPASE, AAA KEYWDS 2 ATPASE, DNA-DEPENDENT ATPASE, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.DELLAS,S.J.NICOLAY,M.J.YOUNG REVDAT 1 13-JAN-16 4R2H 0 JRNL AUTH N.DELLAS,J.C.SNYDER,M.DILLS,S.J.NICOLAY,K.M.KERCHNER, JRNL AUTH 2 S.K.BRUMFIELD,C.M.LAWRENCE,M.J.YOUNG JRNL TITL STRUCTURE-BASED MUTAGENESIS OF STIV B204 REVEALS ESSENTIAL JRNL TITL 2 RESIDUES IN THE VIRION-ASSOCIATED DNA PACKAGING ATPASE. JRNL REF J.VIROL. 2015 JRNL REFN ESSN 1098-5514 JRNL PMID 26699645 JRNL DOI 10.1128/JVI.02435-15 REMARK 2 REMARK 2 RESOLUTION. 1.96 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.65 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 15164 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 762 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 38.6595 - 3.3493 1.00 3006 162 0.1581 0.1998 REMARK 3 2 3.3493 - 2.6586 1.00 2905 131 0.2044 0.2613 REMARK 3 3 2.6586 - 2.3226 1.00 2837 154 0.2111 0.2520 REMARK 3 4 2.3226 - 2.1103 1.00 2828 150 0.1894 0.2492 REMARK 3 5 2.1103 - 1.9600 1.00 2826 165 0.1810 0.2346 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.910 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.74 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 1726 REMARK 3 ANGLE : 0.986 2334 REMARK 3 CHIRALITY : 0.045 259 REMARK 3 PLANARITY : 0.005 285 REMARK 3 DIHEDRAL : 14.361 637 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 4R2H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-AUG-14. REMARK 100 THE RCSB ID CODE IS RCSB086815. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-FEB-13 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 : SSRL REMARK 200 BEAMLINE : BL14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.033 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : SAMPLE TO DETECTOR DISTANCE: 95 REMARK 200 TO 650 MM. MAXIMUM VERTICAL REMARK 200 OFFSET: 60 MM REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15207 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.960 REMARK 200 RESOLUTION RANGE LOW (A) : 43.943 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06100 REMARK 200 FOR THE DATA SET : 17.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.30 REMARK 200 R MERGE FOR SHELL (I) : 0.31500 REMARK 200 R SYM FOR SHELL (I) : 0.31500 REMARK 200 FOR SHELL : 2.500 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 (%): 41.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5M AMMONIUM PHOSPHATE DIBASIC, 0.1M REMARK 280 TRIS-HCL PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 25.93500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.69500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.98000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.69500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.93500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.98000 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 HIS A 206 REMARK 465 HIS A 207 REMARK 465 HIS A 208 REMARK 465 HIS A 209 REMARK 465 HIS A 210 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 GLU A 49 CG CD OE1 OE2 REMARK 470 TYR A 72 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG A 160 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 205 CG ND1 CD2 CE1 NE2 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 HOH A 484 O HOH A 487 2.15 REMARK 500 O HOH A 484 O HOH A 486 2.17 REMARK 500 O HOH A 464 O HOH A 483 2.18 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 TYR A 24 -69.25 -127.31 REMARK 500 LEU A 43 94.56 -68.76 REMARK 500 ILE A 172 -68.99 -121.79 REMARK 500 SER A 173 126.10 -170.02 REMARK 500 TYR A 186 -11.77 75.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 300 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 41 NE2 REMARK 620 2 HIS A 108 NE2 111.8 REMARK 620 3 ASP A 73 OD2 95.4 96.2 REMARK 620 4 ASP A 39 OD2 101.7 95.5 153.9 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 300 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4R2I RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUES 1-204 CORRESPONDS TO UNP ENTRY Q6Q0J1, HOWEVER ONLY REMARK 999 RESIDUES 1-157 IS PRESENT IN Q6Q0J1 AT THE TIME OF PROCESSING THIS REMARK 999 ENTRY DBREF 4R2H A 1 204 UNP Q6Q0J1 Q6Q0J1_9VIRU 1 204 SEQADV 4R2H HIS A 205 UNP Q6Q0J1 EXPRESSION TAG SEQADV 4R2H HIS A 206 UNP Q6Q0J1 EXPRESSION TAG SEQADV 4R2H HIS A 207 UNP Q6Q0J1 EXPRESSION TAG SEQADV 4R2H HIS A 208 UNP Q6Q0J1 EXPRESSION TAG SEQADV 4R2H HIS A 209 UNP Q6Q0J1 EXPRESSION TAG SEQADV 4R2H HIS A 210 UNP Q6Q0J1 EXPRESSION TAG SEQRES 1 A 210 MET ASN PRO ASP ASP ILE VAL VAL ILE ILE GLY ARG LYS SEQRES 2 A 210 ARG SER GLY LYS SER TYR LEU ILE LYS HIS TYR PHE ILE SEQRES 3 A 210 PRO VAL LEU LYS ALA HIS LYS ILE SER TYR ILE ILE ASP SEQRES 4 A 210 ASP HIS ASN LEU LEU ARG SER GLY SER GLU TYR SER LYS SEQRES 5 A 210 PHE GLY TYR ASN VAL VAL THR LEU SER ASP ILE VAL SER SEQRES 6 A 210 LYS GLN TYR VAL VAL VAL TYR ASP ARG GLU LYS ASN ASP SEQRES 7 A 210 VAL PHE PHE GLU LYS LEU TRP ASN GLY ALA LYS LEU HIS SEQRES 8 A 210 ALA LYS LYS TRP GLY THR SER VAL LEU ILE ILE ASP GLU SEQRES 9 A 210 ALA TYR TYR HIS PHE LYS TYR ARG GLN LYS VAL THR PRO SEQRES 10 A 210 ALA ILE ASP GLU ALA LEU HIS ALA ASN ARG HIS ALA GLY SEQRES 11 A 210 ILE GLY LEU ILE LEU SER THR GLN ARG VAL TYR ASP LEU SEQRES 12 A 210 MET PRO ILE VAL TYR LYS GLN ALA ASP LEU ILE ILE MET SEQRES 13 A 210 PHE TYR THR ARG GLU PRO ASN GLU LEU LYS TRP ILE SER SEQRES 14 A 210 LYS TYR ILE SER THR GLU ALA ALA GLU LYS VAL LYS THR SEQRES 15 A 210 LEU LYS GLN TYR TYR PHE LEU ILE TYR ASP VAL ASN SER SEQRES 16 A 210 GLN MET ILE LYS ILE HIS LYS PRO ILE HIS HIS HIS HIS SEQRES 17 A 210 HIS HIS HET ZN A 300 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ FORMUL 3 HOH *89(H2 O) HELIX 1 1 GLY A 16 TYR A 24 1 9 HELIX 2 2 TYR A 24 HIS A 32 1 9 HELIX 3 3 TYR A 50 GLY A 54 5 5 HELIX 4 4 THR A 59 LYS A 66 1 8 HELIX 5 5 ASN A 77 GLY A 96 1 20 HELIX 6 6 ALA A 105 LYS A 110 1 6 HELIX 7 7 THR A 116 ALA A 125 1 10 HELIX 8 8 ALA A 125 GLY A 130 1 6 HELIX 9 9 ARG A 139 LEU A 143 5 5 HELIX 10 10 MET A 144 ALA A 151 1 8 HELIX 11 11 GLU A 161 ILE A 172 1 12 HELIX 12 12 SER A 173 LYS A 181 1 9 SHEET 1 A 8 TYR A 68 TYR A 72 0 SHEET 2 A 8 TYR A 36 ASP A 40 1 N ILE A 38 O VAL A 71 SHEET 3 A 8 SER A 98 ILE A 102 1 O ILE A 101 N ILE A 37 SHEET 4 A 8 ILE A 131 THR A 137 1 O GLY A 132 N LEU A 100 SHEET 5 A 8 ILE A 6 ILE A 10 1 N VAL A 7 O LEU A 133 SHEET 6 A 8 LEU A 153 PHE A 157 1 O ILE A 155 N VAL A 8 SHEET 7 A 8 PHE A 188 ASP A 192 -1 O LEU A 189 N MET A 156 SHEET 8 A 8 MET A 197 HIS A 201 -1 O HIS A 201 N PHE A 188 LINK NE2 HIS A 41 ZN ZN A 300 1555 1555 1.92 LINK NE2 HIS A 108 ZN ZN A 300 1555 1555 1.98 LINK OD2 ASP A 73 ZN ZN A 300 1555 1555 2.10 LINK OD2 ASP A 39 ZN ZN A 300 1555 1555 2.10 SITE 1 AC1 4 ASP A 39 HIS A 41 ASP A 73 HIS A 108 CRYST1 51.870 57.960 67.390 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 0.019279 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017253 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014839 0.00000 MASTER 278 0 1 12 8 0 1 6 0 0 0 17 END