HEADER VIRAL PROTEIN 15-DEC-14 4XAL TITLE CRYSTAL STRUCTURE OF THE CONSERVED CORE DOMAIN OF VP22 FROM HSV-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TEGUMENT PROTEIN VP22; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CORE DOMAIN (UNP RESIDUES 174-281); COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: PEPTIDE SSGVDL; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN HERPESVIRUS 1 (STRAIN 17); SOURCE 3 ORGANISM_COMMON: HHV-1; SOURCE 4 ORGANISM_TAXID: 10299; SOURCE 5 STRAIN: 17; SOURCE 6 GENE: UL49; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HUMAN HERPESVIRUS 1 (STRAIN 17); SOURCE 11 ORGANISM_TAXID: 10299; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS VP22, HSV-1, MHV-68, ORF52, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.HEW,S.L.DAHLROTH,P.NORDLUND REVDAT 2 20-MAR-24 4XAL 1 SOURCE JRNL REMARK REVDAT 1 24-JUN-15 4XAL 0 JRNL AUTH K.HEW,S.L.DAHLROTH,L.X.PAN,T.CORNVIK,P.NORDLUND JRNL TITL VP22 CORE DOMAIN FROM HERPES SIMPLEX VIRUS 1 REVEALS A JRNL TITL 2 SURPRISING STRUCTURAL CONSERVATION IN BOTH THE ALPHA- AND JRNL TITL 3 GAMMAHERPESVIRINAE SUBFAMILIES. JRNL REF J.GEN.VIROL. V. 96 1436 2015 JRNL REFN ESSN 1465-2099 JRNL PMID 26068188 JRNL DOI 10.1099/VIR.0.000078 REMARK 2 REMARK 2 RESOLUTION. 1.87 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) 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) : 1.87 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.92 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 11582 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 580 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 24.9255 - 2.9662 0.98 2859 152 0.2054 0.2578 REMARK 3 2 2.9662 - 2.3549 0.99 2745 144 0.2146 0.2397 REMARK 3 3 2.3549 - 2.0574 1.00 2715 143 0.2016 0.2340 REMARK 3 4 2.0574 - 1.8694 1.00 2683 141 0.2197 0.2751 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.040 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 : 0.007 768 REMARK 3 ANGLE : 0.964 1041 REMARK 3 CHIRALITY : 0.040 118 REMARK 3 PLANARITY : 0.006 137 REMARK 3 DIHEDRAL : 13.158 290 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 4XAL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-DEC-14. REMARK 100 THE DEPOSITION ID IS D_1000205347. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAY-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL13C1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9762 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11585 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.870 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 10.30 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.87 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 10.50 REMARK 200 R MERGE FOR SHELL (I) : 0.28900 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: SIRAS REMARK 200 SOFTWARE USED: PHASER 2.5.6, PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40% PEG 300 AND 0.1 M PHOSPHATE REMARK 280 CITRATE PH 5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 35.88167 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 71.76333 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 53.82250 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 89.70417 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 17.94083 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 35.88167 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 71.76333 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 89.70417 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 53.82250 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 17.94083 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 MET A 1 REMARK 465 HIS A 2 REMARK 465 HIS A 3 REMARK 465 HIS A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 REMARK 465 SER A 8 REMARK 465 SER A 9 REMARK 465 GLY A 10 REMARK 465 VAL A 11 REMARK 465 ASP A 12 REMARK 465 LEU A 13 REMARK 465 GLY A 14 REMARK 465 THR A 15 REMARK 465 GLU A 16 REMARK 465 ASN A 17 REMARK 465 LEU A 18 REMARK 465 TYR A 19 REMARK 465 PHE A 20 REMARK 465 PRO A 111 REMARK 465 ASP A 112 REMARK 465 VAL A 113 REMARK 465 VAL A 114 REMARK 465 GLN A 115 REMARK 465 ASP A 116 REMARK 465 VAL A 117 REMARK 465 ASP A 118 REMARK 465 ALA A 119 REMARK 465 ALA A 120 REMARK 465 THR A 121 REMARK 465 ALA A 122 REMARK 465 THR A 123 REMARK 465 ARG A 124 REMARK 465 GLY A 125 REMARK 465 ARG A 126 REMARK 465 SER A 127 REMARK 465 ALA A 128 REMARK 465 ALA A 129 REMARK 465 SER A 130 REMARK 465 ARG A 131 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 237 O HOH A 255 2.17 REMARK 500 REMARK 500 REMARK: NULL DBREF 4XAL A 24 131 UNP P10233 VP22_HHV11 174 281 DBREF 4XAL B 8 13 PDB 4XAL 4XAL 8 13 SEQADV 4XAL MET A 1 UNP P10233 EXPRESSION TAG SEQADV 4XAL HIS A 2 UNP P10233 EXPRESSION TAG SEQADV 4XAL HIS A 3 UNP P10233 EXPRESSION TAG SEQADV 4XAL HIS A 4 UNP P10233 EXPRESSION TAG SEQADV 4XAL HIS A 5 UNP P10233 EXPRESSION TAG SEQADV 4XAL HIS A 6 UNP P10233 EXPRESSION TAG SEQADV 4XAL HIS A 7 UNP P10233 EXPRESSION TAG SEQADV 4XAL SER A 8 UNP P10233 EXPRESSION TAG SEQADV 4XAL SER A 9 UNP P10233 EXPRESSION TAG SEQADV 4XAL GLY A 10 UNP P10233 EXPRESSION TAG SEQADV 4XAL VAL A 11 UNP P10233 EXPRESSION TAG SEQADV 4XAL ASP A 12 UNP P10233 EXPRESSION TAG SEQADV 4XAL LEU A 13 UNP P10233 EXPRESSION TAG SEQADV 4XAL GLY A 14 UNP P10233 EXPRESSION TAG SEQADV 4XAL THR A 15 UNP P10233 EXPRESSION TAG SEQADV 4XAL GLU A 16 UNP P10233 EXPRESSION TAG SEQADV 4XAL ASN A 17 UNP P10233 EXPRESSION TAG SEQADV 4XAL LEU A 18 UNP P10233 EXPRESSION TAG SEQADV 4XAL TYR A 19 UNP P10233 EXPRESSION TAG SEQADV 4XAL PHE A 20 UNP P10233 EXPRESSION TAG SEQADV 4XAL GLN A 21 UNP P10233 EXPRESSION TAG SEQADV 4XAL SER A 22 UNP P10233 EXPRESSION TAG SEQADV 4XAL MET A 23 UNP P10233 EXPRESSION TAG SEQRES 1 A 131 MET HIS HIS HIS HIS HIS HIS SER SER GLY VAL ASP LEU SEQRES 2 A 131 GLY THR GLU ASN LEU TYR PHE GLN SER MET ARG LYS LEU SEQRES 3 A 131 HIS PHE SER THR ALA PRO PRO ASN PRO ASP ALA PRO TRP SEQRES 4 A 131 THR PRO ARG VAL ALA GLY PHE ASN LYS ARG VAL PHE CYS SEQRES 5 A 131 ALA ALA VAL GLY ARG LEU ALA ALA MET HIS ALA ARG MET SEQRES 6 A 131 ALA ALA VAL GLN LEU TRP ASP MET SER ARG PRO ARG THR SEQRES 7 A 131 ASP GLU ASP LEU ASN GLU LEU LEU GLY ILE THR THR ILE SEQRES 8 A 131 ARG VAL THR VAL CYS GLU GLY LYS ASN LEU LEU GLN ARG SEQRES 9 A 131 ALA ASN GLU LEU VAL ASN PRO ASP VAL VAL GLN ASP VAL SEQRES 10 A 131 ASP ALA ALA THR ALA THR ARG GLY ARG SER ALA ALA SER SEQRES 11 A 131 ARG SEQRES 1 B 6 SER SER GLY VAL ASP LEU FORMUL 3 HOH *74(H2 O) HELIX 1 AA1 THR A 40 ARG A 75 1 36 HELIX 2 AA2 THR A 78 THR A 89 1 12 HELIX 3 AA3 GLU A 97 LYS A 99 5 3 HELIX 4 AA4 ASN A 100 LEU A 108 1 9 SHEET 1 AA1 2 ILE A 91 THR A 94 0 SHEET 2 AA1 2 SER B 9 ASP B 12 -1 O VAL B 11 N ARG A 92 CRYST1 64.940 64.940 107.645 90.00 90.00 120.00 P 61 2 2 12 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 0.015399 0.008891 0.000000 0.00000 SCALE2 0.000000 0.017781 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009290 0.00000