HEADER VIRAL PROTEIN 19-AUG-14 4W5X TITLE THE STRUCTURE OF VACCINA VIRUS H7 PROTEIN DISPLAYS A NOVEL TITLE 2 PHOSPHOINOSITIDE BINDING FOLD REQUIRED FOR MEMBRANE BIOGENESIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: LATE PROTEIN H7; COMPND 3 CHAIN: B, A; COMPND 4 FRAGMENT: UNP RESIDUES 1-118; COMPND 5 SYNONYM: PROTEIN H8; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VACCINIA VIRUS; SOURCE 3 ORGANISM_COMMON: VACV; SOURCE 4 ORGANISM_TAXID: 10254; SOURCE 5 STRAIN: WESTERN RESERVE; SOURCE 6 GENE: VACWR105, H7R; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21GOLDDE3 KEYWDS PROTEIN PHOSPHOINOSITIDE, MEMBRANE BIOGENESIS, POXVIRUS, LIPID KEYWDS 2 BINDING, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.KOLLI,J.DENG REVDAT 5 27-DEC-23 4W5X 1 REMARK REVDAT 4 11-DEC-19 4W5X 1 REMARK REVDAT 3 13-SEP-17 4W5X 1 SOURCE JRNL REMARK REVDAT 2 04-FEB-15 4W5X 1 JRNL REVDAT 1 31-DEC-14 4W5X 0 JRNL AUTH S.KOLLI,X.MENG,X.WU,D.SHENGJULER,C.E.CAMERON,Y.XIANG,J.DENG JRNL TITL STRUCTURE-FUNCTION ANALYSIS OF VACCINIA VIRUS H7 PROTEIN JRNL TITL 2 REVEALS A NOVEL PHOSPHOINOSITIDE BINDING FOLD ESSENTIAL FOR JRNL TITL 3 POXVIRUS REPLICATION. JRNL REF J.VIROL. V. 89 2209 2015 JRNL REFN ESSN 1098-5514 JRNL PMID 25473060 JRNL DOI 10.1128/JVI.03073-14 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6_289) 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.49 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.150 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 3 NUMBER OF REFLECTIONS : 16276 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.930 REMARK 3 FREE R VALUE TEST SET COUNT : 1616 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 39.4928 - 4.3109 0.99 1634 179 0.1675 0.2000 REMARK 3 2 4.3109 - 3.4223 1.00 1570 175 0.1710 0.2192 REMARK 3 3 3.4223 - 2.9899 0.98 1554 170 0.2086 0.2531 REMARK 3 4 2.9899 - 2.7166 0.97 1522 172 0.2239 0.2589 REMARK 3 5 2.7166 - 2.5219 0.97 1512 171 0.2141 0.2905 REMARK 3 6 2.5219 - 2.3732 0.96 1501 163 0.2098 0.2565 REMARK 3 7 2.3732 - 2.2544 0.93 1436 156 0.2039 0.3158 REMARK 3 8 2.2544 - 2.1563 0.90 1385 151 0.2069 0.2710 REMARK 3 9 2.1563 - 2.0733 0.87 1367 152 0.2028 0.2979 REMARK 3 10 2.0733 - 2.0017 0.78 1179 127 0.2182 0.3215 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 : 0.32 REMARK 3 B_SOL : 40.75 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.840 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) : 15.85650 REMARK 3 B22 (A**2) : -2.30280 REMARK 3 B33 (A**2) : -13.55370 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.75710 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 : 0.007 1933 REMARK 3 ANGLE : 0.957 2592 REMARK 3 CHIRALITY : 0.064 290 REMARK 3 PLANARITY : 0.003 327 REMARK 3 DIHEDRAL : 13.786 736 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 4W5X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-AUG-14. REMARK 100 THE DEPOSITION ID IS D_1000203244. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-AUG-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.8 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16966 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 97.6 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.5 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 : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.08M BIS-TRIS PHOSPHATE/CITRIC ACID, REMARK 280 18% (W/V) PEG 3350, PH 8.8, EVAPORATION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 56.39250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.10350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 56.39250 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 17.10350 REMARK 290 SMTRY3 4 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 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 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 HIS B 0 REMARK 465 MET B 1 REMARK 465 SER B 118 REMARK 465 HIS A 0 REMARK 465 MET A 1 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 B 2 CG CD OE1 OE2 REMARK 470 LYS B 5 CB CG CD CE NZ REMARK 470 ARG B 34 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 45 CG CD CE NZ REMARK 470 ASN B 57 OD1 ND2 REMARK 470 LYS B 112 CG CD CE NZ REMARK 470 LYS B 113 NZ REMARK 470 ARG B 115 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 117 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 2 CG CD OE1 OE2 REMARK 470 LYS A 5 CB CG CD CE NZ REMARK 470 LYS A 33 CD CE NZ REMARK 470 ARG A 34 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 45 CD CE NZ REMARK 470 GLN A 48 CG CD OE1 NE2 REMARK 470 ASN A 57 ND2 REMARK 470 THR A 67 CB OG1 CG2 REMARK 470 LYS A 112 CG CD CE NZ REMARK 470 ARG A 115 CZ NH1 NH2 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 THR B 13 -85.25 -124.84 REMARK 500 ASP B 96 86.25 -154.44 REMARK 500 THR A 13 -85.93 -124.06 REMARK 500 ASP A 96 83.16 -162.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4W5Y RELATED DB: PDB REMARK 900 RELATED ID: 4W60 RELATED DB: PDB DBREF 4W5X B 1 118 UNP P08586 H7_VACCW 1 118 DBREF 4W5X A 1 118 UNP P08586 H7_VACCW 1 118 SEQADV 4W5X HIS B 0 UNP P08586 EXPRESSION TAG SEQADV 4W5X SER B 89 UNP P08586 CYS 89 ENGINEERED MUTATION SEQADV 4W5X HIS A 0 UNP P08586 EXPRESSION TAG SEQADV 4W5X SER A 89 UNP P08586 CYS 89 ENGINEERED MUTATION SEQRES 1 B 119 HIS MET GLU MET ASP LYS ARG MET LYS SER LEU ALA MET SEQRES 2 B 119 THR ALA PHE PHE GLY GLU LEU SER THR LEU ASP ILE MET SEQRES 3 B 119 ALA LEU ILE MET SER ILE PHE LYS ARG HIS PRO ASN ASN SEQRES 4 B 119 THR ILE PHE SER VAL ASP LYS ASP GLY GLN PHE MET ILE SEQRES 5 B 119 ASP PHE GLU TYR ASP ASN TYR LYS ALA SER GLN TYR LEU SEQRES 6 B 119 ASP LEU THR LEU THR PRO ILE SER GLY ASP GLU CYS LYS SEQRES 7 B 119 THR HIS ALA SER SER ILE ALA GLU GLN LEU ALA SER VAL SEQRES 8 B 119 ASP ILE ILE LYS GLU ASP ILE SER GLU TYR ILE LYS THR SEQRES 9 B 119 THR PRO ARG LEU LYS ARG PHE ILE LYS LYS TYR ARG ASN SEQRES 10 B 119 ARG SER SEQRES 1 A 119 HIS MET GLU MET ASP LYS ARG MET LYS SER LEU ALA MET SEQRES 2 A 119 THR ALA PHE PHE GLY GLU LEU SER THR LEU ASP ILE MET SEQRES 3 A 119 ALA LEU ILE MET SER ILE PHE LYS ARG HIS PRO ASN ASN SEQRES 4 A 119 THR ILE PHE SER VAL ASP LYS ASP GLY GLN PHE MET ILE SEQRES 5 A 119 ASP PHE GLU TYR ASP ASN TYR LYS ALA SER GLN TYR LEU SEQRES 6 A 119 ASP LEU THR LEU THR PRO ILE SER GLY ASP GLU CYS LYS SEQRES 7 A 119 THR HIS ALA SER SER ILE ALA GLU GLN LEU ALA SER VAL SEQRES 8 A 119 ASP ILE ILE LYS GLU ASP ILE SER GLU TYR ILE LYS THR SEQRES 9 A 119 THR PRO ARG LEU LYS ARG PHE ILE LYS LYS TYR ARG ASN SEQRES 10 A 119 ARG SER FORMUL 3 HOH *168(H2 O) HELIX 1 AA1 ASP B 4 THR B 13 1 10 HELIX 2 AA2 SER B 20 LYS B 33 1 14 HELIX 3 AA3 LYS B 59 ASP B 65 5 7 HELIX 4 AA4 ASP B 74 HIS B 79 1 6 HELIX 5 AA5 HIS B 79 ASP B 96 1 18 HELIX 6 AA6 ASP B 96 THR B 103 1 8 HELIX 7 AA7 THR B 104 ARG B 115 1 12 HELIX 8 AA8 ASP A 4 THR A 13 1 10 HELIX 9 AA9 SER A 20 LYS A 33 1 14 HELIX 10 AB1 LYS A 59 ASP A 65 5 7 HELIX 11 AB2 SER A 72 HIS A 79 1 8 HELIX 12 AB3 HIS A 79 ASP A 96 1 18 HELIX 13 AB4 ASP A 96 THR A 104 1 9 HELIX 14 AB5 THR A 104 ARG A 115 1 12 SHEET 1 AA1 3 PHE B 49 GLU B 54 0 SHEET 2 AA1 3 ASN B 38 VAL B 43 -1 N ASN B 38 O GLU B 54 SHEET 3 AA1 3 THR B 69 PRO B 70 -1 O THR B 69 N VAL B 43 SHEET 1 AA2 3 PHE A 49 GLU A 54 0 SHEET 2 AA2 3 ASN A 38 VAL A 43 -1 N ILE A 40 O ASP A 52 SHEET 3 AA2 3 THR A 69 PRO A 70 -1 O THR A 69 N VAL A 43 SSBOND 1 CYS B 76 CYS A 76 1555 1556 2.06 CRYST1 112.785 34.207 67.200 90.00 99.57 90.00 C 1 2 1 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 0.008866 0.000000 0.001495 0.00000 SCALE2 0.000000 0.029234 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015091 0.00000