HEADER DNA BINDING PROTEIN 25-DEC-19 6LMH TITLE STRUCTURE OF AN ASFV-DERIVED HISTONE-LIKE PROTEIN PA104R COMPND MOL_ID: 1; COMPND 2 MOLECULE: PA104R; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PA104R, A104R CDS PROTEIN,BA71V-A104R,HISTONE-LIKE PROTEIN, COMPND 5 PA104R; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AFRICAN SWINE FEVER VIRUS; SOURCE 3 ORGANISM_COMMON: ASFV; SOURCE 4 ORGANISM_TAXID: 10497; SOURCE 5 GENE: A104R, A104R CDS, BA71V-A104R, AFSV47SS_0056, ASFV-GEORGIA_4- SOURCE 6 058; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS APO STATE, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.WANG,J.QI,Y.CHAI,F.GAO REVDAT 3 27-MAR-24 6LMH 1 REMARK REVDAT 2 03-JUN-20 6LMH 1 JRNL REVDAT 1 13-MAY-20 6LMH 0 JRNL AUTH R.LIU,Y.SUN,Y.CHAI,S.LI,S.LI,L.WANG,J.SU,S.YU,J.YAN,F.GAO, JRNL AUTH 2 G.ZHANG,H.J.QIU,G.F.GAO,J.QI,H.WANG JRNL TITL THE STRUCTURAL BASIS OF AFRICAN SWINE FEVER VIRUS PA104R JRNL TITL 2 BINDING TO DNA AND ITS INHIBITION BY STILBENE DERIVATIVES. JRNL REF PROC.NATL.ACAD.SCI.USA V. 117 11000 2020 JRNL REFN ESSN 1091-6490 JRNL PMID 32358196 JRNL DOI 10.1073/PNAS.1922523117 REMARK 2 REMARK 2 RESOLUTION. 2.81 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.15.2_3472: ???) 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) : 2.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.09 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 7551 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.256 REMARK 3 R VALUE (WORKING SET) : 0.253 REMARK 3 FREE R VALUE : 0.299 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 393 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 42.0900 - 4.0446 1.00 2582 131 0.2276 0.2584 REMARK 3 2 4.0446 - 3.2106 1.00 2420 156 0.2677 0.3273 REMARK 3 3 3.2106 - 2.8050 0.89 2156 106 0.2997 0.3597 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) : 0.430 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.170 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 : 0.009 1582 REMARK 3 ANGLE : 0.905 2140 REMARK 3 CHIRALITY : 0.060 256 REMARK 3 PLANARITY : 0.006 272 REMARK 3 DIHEDRAL : 18.975 624 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 6LMH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-DEC-19. REMARK 100 THE DEPOSITION ID IS D_1300015060. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7855 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 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 (%) : 99.6 REMARK 200 DATA REDUNDANCY : 18.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 48.1330 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: PHASES REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M CITRIC ACID, PH 4.5, 2.4 M REMARK 280 AMMONIUM SULFATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 100.39733 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 50.19867 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 50.19867 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 100.39733 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: 4750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 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 HIS 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 MET A 7 REMARK 465 SER A 8 REMARK 465 THR A 9 REMARK 465 LYS A 10 REMARK 465 LYS A 11 REMARK 465 HIS B 1 REMARK 465 HIS B 2 REMARK 465 HIS B 3 REMARK 465 HIS B 4 REMARK 465 HIS B 5 REMARK 465 HIS B 6 REMARK 465 MET B 7 REMARK 465 SER B 8 REMARK 465 THR B 9 REMARK 465 LYS B 10 REMARK 465 LYS B 11 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 PRO A 60 43.80 -89.91 REMARK 500 PRO B 60 47.94 -94.09 REMARK 500 REMARK 500 REMARK: NULL DBREF1 6LMH A 7 110 UNP A0A0A1E0L7_ASF DBREF2 6LMH A A0A0A1E0L7 1 104 DBREF1 6LMH B 7 110 UNP A0A0A1E0L7_ASF DBREF2 6LMH B A0A0A1E0L7 1 104 SEQADV 6LMH HIS A 1 UNP A0A0A1E0L EXPRESSION TAG SEQADV 6LMH HIS A 2 UNP A0A0A1E0L EXPRESSION TAG SEQADV 6LMH HIS A 3 UNP A0A0A1E0L EXPRESSION TAG SEQADV 6LMH HIS A 4 UNP A0A0A1E0L EXPRESSION TAG SEQADV 6LMH HIS A 5 UNP A0A0A1E0L EXPRESSION TAG SEQADV 6LMH HIS A 6 UNP A0A0A1E0L EXPRESSION TAG SEQADV 6LMH HIS B 1 UNP A0A0A1E0L EXPRESSION TAG SEQADV 6LMH HIS B 2 UNP A0A0A1E0L EXPRESSION TAG SEQADV 6LMH HIS B 3 UNP A0A0A1E0L EXPRESSION TAG SEQADV 6LMH HIS B 4 UNP A0A0A1E0L EXPRESSION TAG SEQADV 6LMH HIS B 5 UNP A0A0A1E0L EXPRESSION TAG SEQADV 6LMH HIS B 6 UNP A0A0A1E0L EXPRESSION TAG SEQRES 1 A 110 HIS HIS HIS HIS HIS HIS MET SER THR LYS LYS LYS PRO SEQRES 2 A 110 THR ILE THR LYS GLN GLU LEU TYR SER LEU VAL ALA ALA SEQRES 3 A 110 ASP THR GLN LEU ASN LYS ALA LEU ILE GLU ARG ILE PHE SEQRES 4 A 110 THR SER GLN GLN LYS ILE ILE GLN ASN ALA LEU LYS HIS SEQRES 5 A 110 ASN GLN GLU VAL ILE ILE PRO PRO GLY ILE LYS PHE THR SEQRES 6 A 110 VAL VAL THR VAL LYS ALA LYS PRO ALA ARG GLN GLY HIS SEQRES 7 A 110 ASN PRO ALA THR GLY GLU PRO ILE GLN ILE LYS ALA LYS SEQRES 8 A 110 PRO GLU HIS LYS ALA VAL LYS ILE ARG ALA LEU LYS PRO SEQRES 9 A 110 VAL HIS ASP MET LEU ASN SEQRES 1 B 110 HIS HIS HIS HIS HIS HIS MET SER THR LYS LYS LYS PRO SEQRES 2 B 110 THR ILE THR LYS GLN GLU LEU TYR SER LEU VAL ALA ALA SEQRES 3 B 110 ASP THR GLN LEU ASN LYS ALA LEU ILE GLU ARG ILE PHE SEQRES 4 B 110 THR SER GLN GLN LYS ILE ILE GLN ASN ALA LEU LYS HIS SEQRES 5 B 110 ASN GLN GLU VAL ILE ILE PRO PRO GLY ILE LYS PHE THR SEQRES 6 B 110 VAL VAL THR VAL LYS ALA LYS PRO ALA ARG GLN GLY HIS SEQRES 7 B 110 ASN PRO ALA THR GLY GLU PRO ILE GLN ILE LYS ALA LYS SEQRES 8 B 110 PRO GLU HIS LYS ALA VAL LYS ILE ARG ALA LEU LYS PRO SEQRES 9 B 110 VAL HIS ASP MET LEU ASN HELIX 1 AA1 THR A 16 GLN A 29 1 14 HELIX 2 AA2 ASN A 31 HIS A 52 1 22 HELIX 3 AA3 LEU A 102 ASP A 107 1 6 HELIX 4 AA4 MET A 108 ASN A 110 5 3 HELIX 5 AA5 THR B 16 GLN B 29 1 14 HELIX 6 AA6 ASN B 31 LYS B 51 1 21 HELIX 7 AA7 LEU B 102 ASP B 107 1 6 SHEET 1 AA1 3 VAL A 56 ILE A 58 0 SHEET 2 AA1 3 ILE A 62 VAL A 69 -1 O PHE A 64 N VAL A 56 SHEET 3 AA1 3 HIS A 94 ALA A 101 -1 O ALA A 96 N VAL A 67 SHEET 1 AA2 2 ARG A 75 HIS A 78 0 SHEET 2 AA2 2 PRO A 85 ILE A 88 -1 O ILE A 86 N GLY A 77 SHEET 1 AA3 3 VAL B 56 ILE B 58 0 SHEET 2 AA3 3 ILE B 62 VAL B 69 -1 O PHE B 64 N VAL B 56 SHEET 3 AA3 3 HIS B 94 ALA B 101 -1 O LYS B 98 N THR B 65 SHEET 1 AA4 2 ARG B 75 HIS B 78 0 SHEET 2 AA4 2 PRO B 85 ILE B 88 -1 O ILE B 88 N ARG B 75 CISPEP 1 PRO A 59 PRO A 60 0 -3.04 CISPEP 2 PRO B 59 PRO B 60 0 2.63 CRYST1 58.618 58.618 150.596 90.00 90.00 120.00 P 32 2 1 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 0.017060 0.009849 0.000000 0.00000 SCALE2 0.000000 0.019699 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006640 0.00000