HEADER VIRAL PROTEIN 28-SEP-21 7VIV TITLE CRYSTAL STRUCTURE OF THE I73R FROM AFRICAN SWINE FEVER VIRUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: I73R; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: I73R CDS PROTEIN,I73R PROTEIN; COMPND 5 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: I73R CDS, I73R, ASFV-GEORGIA_4-163, ASFV_KYIV_2016_131_00219; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET32A KEYWDS Z-DNA BINDING PROTEIN, ASFV, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.F.SUN,Y.K.WU REVDAT 2 29-MAY-24 7VIV 1 REMARK REVDAT 1 07-SEP-22 7VIV 0 JRNL AUTH L.F.SUN JRNL TITL STRUCTURAL INSIGHT INTO AFRICAN SWINE FEVER VIRUS I73R JRNL TITL 2 PROTEIN REVEALS IT IS A Z-DNA BINDING PROTEIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 19.82 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.780 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 9266 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.180 REMARK 3 FREE R VALUE TEST SET COUNT : 480 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 19.8200 - 2.8800 1.00 2926 161 0.1631 0.2075 REMARK 3 2 2.8800 - 2.2900 1.00 2924 162 0.2397 0.2523 REMARK 3 3 2.2900 - 2.0000 1.00 2936 157 0.2523 0.2847 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) : 30.270 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 61.20 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -11.9414 8.3889 -9.3507 REMARK 3 T TENSOR REMARK 3 T11: 0.3538 T22: 0.3593 REMARK 3 T33: 0.3443 T12: -0.0033 REMARK 3 T13: -0.0689 T23: -0.0041 REMARK 3 L TENSOR REMARK 3 L11: 1.6260 L22: 3.4808 REMARK 3 L33: -0.1843 L12: 0.5102 REMARK 3 L13: -0.2760 L23: -0.5428 REMARK 3 S TENSOR REMARK 3 S11: -0.1809 S12: 0.0473 S13: 0.1972 REMARK 3 S21: -0.4607 S22: 0.1131 S23: 0.3896 REMARK 3 S31: -0.1599 S32: -0.1190 S33: 0.0006 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 7VIV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-OCT-21. REMARK 100 THE DEPOSITION ID IS D_1300024788. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-OCT-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U 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 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9855 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.960 REMARK 200 RESOLUTION RANGE LOW (A) : 44.680 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 10.10 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.0000 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) : 2.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 9.50 REMARK 200 R MERGE FOR SHELL (I) : 0.87500 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LI2SO4, 0.1 M BIS-TRIS PH 5.5, REMARK 280 25% (W/V) PEG3350, EVAPORATION, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 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+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,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 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 44.68000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.79601 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 15.38667 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 44.68000 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 25.79601 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 15.38667 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 44.68000 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 25.79601 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 15.38667 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 51.59202 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 30.77333 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 51.59202 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 30.77333 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 51.59202 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 30.77333 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -60.0 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 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 GLN A 18 40.23 -102.81 REMARK 500 ASN A 50 69.10 -114.72 REMARK 500 REMARK 500 REMARK: NULL DBREF1 7VIV A 1 72 UNP A0A2X0RU36_ASF DBREF2 7VIV A A0A2X0RU36 1 72 DBREF1 7VIV B 1 72 UNP A0A2X0RU36_ASF DBREF2 7VIV B A0A2X0RU36 1 72 SEQRES 1 A 72 MET GLU THR GLN LYS LEU ILE SER MET VAL LYS GLU ALA SEQRES 2 A 72 LEU GLU LYS TYR GLN TYR PRO LEU THR ALA LYS ASN ILE SEQRES 3 A 72 LYS VAL VAL ILE GLN LYS GLU HIS ASN VAL VAL LEU PRO SEQRES 4 A 72 THR GLY SER ILE ASN SER ILE LEU TYR SER ASN SER GLU SEQRES 5 A 72 LEU PHE GLU LYS ILE ASP LYS THR ASN THR ILE TYR PRO SEQRES 6 A 72 PRO LEU TRP ILE ARG LYS ASN SEQRES 1 B 72 MET GLU THR GLN LYS LEU ILE SER MET VAL LYS GLU ALA SEQRES 2 B 72 LEU GLU LYS TYR GLN TYR PRO LEU THR ALA LYS ASN ILE SEQRES 3 B 72 LYS VAL VAL ILE GLN LYS GLU HIS ASN VAL VAL LEU PRO SEQRES 4 B 72 THR GLY SER ILE ASN SER ILE LEU TYR SER ASN SER GLU SEQRES 5 B 72 LEU PHE GLU LYS ILE ASP LYS THR ASN THR ILE TYR PRO SEQRES 6 B 72 PRO LEU TRP ILE ARG LYS ASN FORMUL 3 HOH *64(H2 O) HELIX 1 AA1 MET A 1 TYR A 17 1 17 HELIX 2 AA2 ALA A 23 ASN A 35 1 13 HELIX 3 AA3 PRO A 39 ASN A 50 1 12 HELIX 4 AA4 GLU B 2 TYR B 17 1 16 HELIX 5 AA5 THR B 22 ASN B 35 1 14 HELIX 6 AA6 PRO B 39 ASN B 50 1 12 SHEET 1 AA1 3 LEU A 21 THR A 22 0 SHEET 2 AA1 3 LEU A 67 ARG A 70 -1 O TRP A 68 N LEU A 21 SHEET 3 AA1 3 PHE A 54 LYS A 56 -1 N GLU A 55 O ILE A 69 SHEET 1 AA2 2 PHE B 54 LYS B 56 0 SHEET 2 AA2 2 TRP B 68 ARG B 70 -1 O ILE B 69 N GLU B 55 CISPEP 1 TYR A 64 PRO A 65 0 -7.51 CISPEP 2 TYR B 64 PRO B 65 0 -5.41 CRYST1 89.360 89.360 46.160 90.00 90.00 120.00 H 3 18 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 0.011191 0.006461 0.000000 0.00000 SCALE2 0.000000 0.012922 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021664 0.00000