HEADER VIRAL PROTEIN 09-NOV-17 6BL5 TITLE HEAD DECORATION PROTEIN FROM THE HYPERTHERMOPHILIC PHAGE P74-26 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEAD DECORATION PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS VIRUS P74-26; SOURCE 3 ORGANISM_TAXID: 466052; SOURCE 4 GENE: P74P87; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BETA-TULIP DOMAIN, CAPSID, VIRION, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.P.STONE,B.J.HILBERT,D.HIDALGO,K.T.HALLORAN,B.A.KELCH REVDAT 4 13-MAR-24 6BL5 1 REMARK REVDAT 3 18-JUL-18 6BL5 1 JRNL REVDAT 2 06-JUN-18 6BL5 1 JRNL REVDAT 1 21-FEB-18 6BL5 0 JRNL AUTH N.P.STONE,B.J.HILBERT,D.HIDALGO,K.T.HALLORAN,J.LEE, JRNL AUTH 2 E.J.SONTHEIMER,B.A.KELCH JRNL TITL A HYPERTHERMOPHILIC PHAGE DECORATION PROTEIN SUGGESTS COMMON JRNL TITL 2 EVOLUTIONARY ORIGIN WITH HERPESVIRUS TRIPLEX PROTEINS AND AN JRNL TITL 3 ANTI-CRISPR PROTEIN. JRNL REF STRUCTURE V. 26 936 2018 JRNL REFN ISSN 1878-4186 JRNL PMID 29779790 JRNL DOI 10.1016/J.STR.2018.04.008 REMARK 2 REMARK 2 RESOLUTION. 1.69 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.69 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 16355 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1637 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 25.8441 - 3.8660 0.99 1279 140 0.1425 0.1654 REMARK 3 2 3.8660 - 3.0702 1.00 1253 136 0.1653 0.1890 REMARK 3 3 3.0702 - 2.6825 1.00 1232 141 0.1851 0.2091 REMARK 3 4 2.6825 - 2.4375 1.00 1223 135 0.1897 0.2578 REMARK 3 5 2.4375 - 2.2629 1.00 1228 134 0.1960 0.2380 REMARK 3 6 2.2629 - 2.1295 1.00 1220 138 0.1988 0.2283 REMARK 3 7 2.1295 - 2.0229 1.00 1224 135 0.2022 0.2523 REMARK 3 8 2.0229 - 1.9349 1.00 1211 136 0.2333 0.2950 REMARK 3 9 1.9349 - 1.8604 1.00 1209 132 0.2260 0.2700 REMARK 3 10 1.8604 - 1.7962 1.00 1217 142 0.2495 0.2885 REMARK 3 11 1.7962 - 1.7401 1.00 1212 134 0.2583 0.3039 REMARK 3 12 1.7401 - 1.6904 1.00 1210 134 0.2690 0.2933 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 23.990 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 : 0.010 1046 REMARK 3 ANGLE : 1.046 1439 REMARK 3 CHIRALITY : 0.066 153 REMARK 3 PLANARITY : 0.008 192 REMARK 3 DIHEDRAL : 13.775 614 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 6BL5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1000230997. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : SI ROSENBAUM-ROCK DOUBLE-CRYSTAL REMARK 200 OPTICS : SAGITALLY FOCUSING 2ND CRYSTAL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 V703X REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16355 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.690 REMARK 200 RESOLUTION RANGE LOW (A) : 25.841 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.69 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : 0.82400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: AUTOSOL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL PH 7.0, 20% PEG 3350, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 15.69500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 15.69500 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 15.69500 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: TRIMERIC 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 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 44.75800 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 77.52313 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -44.75800 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 77.52313 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 ASP A 1 REMARK 465 LYS A 2 REMARK 465 ILE A 3 REMARK 465 GLN A 4 REMARK 465 LEU A 5 REMARK 465 PHE A 6 REMARK 465 ARG A 7 REMARK 465 THR A 8 REMARK 465 ILE A 9 REMARK 465 GLY A 10 REMARK 465 ARG A 11 REMARK 465 VAL A 12 REMARK 465 GLN A 13 REMARK 465 TYR A 14 REMARK 465 TRP A 15 REMARK 465 GLU A 16 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 ASP A 88 75.32 -163.73 REMARK 500 GLN A 110 68.96 -109.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 298 DISTANCE = 6.13 ANGSTROMS DBREF 6BL5 A 1 145 UNP A7XXR5 A7XXR5_9CAUD 2 146 SEQRES 1 A 145 ASP LYS ILE GLN LEU PHE ARG THR ILE GLY ARG VAL GLN SEQRES 2 A 145 TYR TRP GLU ARG VAL PRO ARG LEU HIS ALA TYR GLY VAL SEQRES 3 A 145 PHE ALA LEU PRO PHE PRO MET ASP PRO ASP VAL GLU TRP SEQRES 4 A 145 GLY ASN TRP PHE ALA GLY PRO HIS PRO LYS ALA PHE LEU SEQRES 5 A 145 VAL SER VAL HIS PRO SER GLY PRO LYS ALA GLY HIS VAL SEQRES 6 A 145 TYR PRO THR ASP LEU SER ASP PRO ASP SER VAL ALA ASN SEQRES 7 A 145 VAL ILE GLY MET VAL LEU ASP GLY HIS ASP TYR GLU ALA SEQRES 8 A 145 ASP HIS ASN VAL THR VAL THR LEU ARG ALA ALA VAL PRO SEQRES 9 A 145 ILE GLU TYR VAL GLN GLN GLY ILE GLU ALA PRO PRO LEU SEQRES 10 A 145 GLN PRO ASP PRO ALA VAL LEU ASN ALA ALA PRO GLN LEU SEQRES 11 A 145 LYS LEU LYS VAL ILE LYS GLY HIS TYR PHE PHE ASP TYR SEQRES 12 A 145 THR ARG FORMUL 2 HOH *98(H2 O) HELIX 1 AA1 LEU A 21 GLY A 25 5 5 HELIX 2 AA2 GLU A 38 PHE A 43 5 6 HELIX 3 AA3 ASP A 72 ASN A 78 1 7 HELIX 4 AA4 GLU A 106 VAL A 108 5 3 HELIX 5 AA5 ASP A 120 LYS A 131 1 12 SHEET 1 AA1 4 PHE A 27 PRO A 32 0 SHEET 2 AA1 4 ASN A 94 PRO A 104 -1 O VAL A 95 N PHE A 31 SHEET 3 AA1 4 HIS A 138 ASP A 142 -1 O TYR A 139 N VAL A 103 SHEET 4 AA1 4 LYS A 133 ILE A 135 -1 N LYS A 133 O PHE A 140 SHEET 1 AA2 3 VAL A 65 PRO A 67 0 SHEET 2 AA2 3 PHE A 51 VAL A 55 -1 N SER A 54 O TYR A 66 SHEET 3 AA2 3 VAL A 79 VAL A 83 -1 O ILE A 80 N VAL A 53 CRYST1 89.516 89.516 31.390 90.00 90.00 120.00 P 63 6 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 0.011171 0.006450 0.000000 0.00000 SCALE2 0.000000 0.012899 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031857 0.00000