HEADER VIRAL PROTEIN 29-DEC-22 8HW5 TITLE CRYSTAL STRUCTURE OF AFRICAN SWINE FEVER VIRUS CP312R COMPND MOL_ID: 1; COMPND 2 MOLECULE: CP312R; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CP312R CDS PROTEIN,CP312R PROTEIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AFRICAN SWINE FEVER VIRUS; SOURCE 3 ORGANISM_TAXID: 10497; SOURCE 4 GENE: CP312R CDS, CP312R, ASFV-GEORGIA_4-120; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CP312R, AFRICAN SWINE FEVER VIRUS, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR W.M.WANG,Z.Y.WANG,D.FU,Y.GUO REVDAT 1 17-JAN-24 8HW5 0 JRNL AUTH Y.T.HAGOSS,D.D.SHEN,W.M.WANG,Y.GUO,Z.G.BU,D.M.ZHAO JRNL TITL AFRICAN SWINE FEVER VIRUS CP312R IS ESSENTIAL FOR VIRUS JRNL TITL 2 REPLICATION AND INHIBITS HOST PROTEIN EXPRESSION BY JRNL TITL 3 INTERACTING WITH RPS27A JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 13709 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1372 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 24.0700 - 4.9400 0.98 1256 130 0.1721 0.2028 REMARK 3 2 4.9400 - 3.9200 0.99 1239 131 0.1488 0.2094 REMARK 3 3 3.9200 - 3.4300 1.00 1230 142 0.1816 0.2178 REMARK 3 4 3.4300 - 3.1200 1.00 1242 143 0.2017 0.2477 REMARK 3 5 3.1200 - 2.8900 1.00 1248 126 0.2023 0.2609 REMARK 3 6 2.8900 - 2.7200 1.00 1215 155 0.2156 0.2695 REMARK 3 7 2.7200 - 2.5900 1.00 1233 136 0.2075 0.3177 REMARK 3 8 2.5900 - 2.4700 1.00 1246 130 0.2100 0.2435 REMARK 3 9 2.4700 - 2.3800 1.00 1211 140 0.2035 0.2573 REMARK 3 10 2.3800 - 2.3000 0.97 1217 139 0.2182 0.2749 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.150 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 : 0.004 2133 REMARK 3 ANGLE : 0.587 2874 REMARK 3 CHIRALITY : 0.047 327 REMARK 3 PLANARITY : 0.005 375 REMARK 3 DIHEDRAL : 5.122 270 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): 0.4168 -0.9292 12.7149 REMARK 3 T TENSOR REMARK 3 T11: 0.1530 T22: 0.1873 REMARK 3 T33: 0.1751 T12: 0.0053 REMARK 3 T13: 0.0009 T23: -0.0330 REMARK 3 L TENSOR REMARK 3 L11: 1.1083 L22: 1.8658 REMARK 3 L33: 1.2154 L12: 0.0930 REMARK 3 L13: -0.1676 L23: -0.4643 REMARK 3 S TENSOR REMARK 3 S11: 0.0148 S12: -0.1172 S13: 0.0118 REMARK 3 S21: 0.0264 S22: -0.0468 S23: -0.0228 REMARK 3 S31: -0.0944 S32: 0.1050 S33: 0.0400 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 8HW5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1300034261. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-NOV-21 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 : SSRF REMARK 200 BEAMLINE : BL10U2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9785 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13790 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 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 (%) : 98.8 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.99200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.25000 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: ALPHAFOLD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MAGNESIUM CHLORIDE BIS-TRIS PEG 3350, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 39.89950 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: 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 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 LEU A 35 REMARK 465 ARG A 36 REMARK 465 THR A 37 REMARK 465 ALA A 38 REMARK 465 LYS A 39 REMARK 465 ARG A 40 REMARK 465 ASN A 41 REMARK 465 THR A 42 REMARK 465 SER A 175 REMARK 465 ASN A 176 REMARK 465 SER A 177 REMARK 465 ALA A 178 REMARK 465 VAL A 179 REMARK 465 LYS A 180 REMARK 465 ASN A 181 REMARK 465 ALA A 182 REMARK 465 ASP A 183 REMARK 465 LYS A 184 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 LEU A 118 -30.03 -139.86 REMARK 500 SER A 223 -154.82 -118.97 REMARK 500 REMARK 500 REMARK: NULL DBREF1 8HW5 A 1 279 UNP A0A2X0RVH4_ASF DBREF2 8HW5 A A0A2X0RVH4 1 279 SEQRES 1 A 279 MET THR THR HIS ILE PHE HIS ALA ASP ASP LEU LEU GLN SEQRES 2 A 279 ALA LEU GLN GLN ALA LYS ALA GLU LYS ASN PHE SER SER SEQRES 3 A 279 VAL PHE SER LEU ASP TRP ASP LYS LEU ARG THR ALA LYS SEQRES 4 A 279 ARG ASN THR THR VAL LYS TYR VAL THR VAL ASN VAL ILE SEQRES 5 A 279 VAL LYS GLY LYS LYS ALA PRO LEU MET PHE ASN PHE GLN SEQRES 6 A 279 ASN GLU LYS HIS VAL GLY THR ILE PRO PRO SER THR ASP SEQRES 7 A 279 GLU GLU VAL ILE ARG MET ASN ALA GLU ASN PRO LYS PHE SEQRES 8 A 279 LEU VAL LYS LYS ARG ASP ARG ASP PRO CYS LEU GLN PHE SEQRES 9 A 279 ASN LYS TYR LYS ILE SER PRO PRO LEU GLU ASP ASP GLY SEQRES 10 A 279 LEU THR VAL LYS LYS ASN GLU GLN GLY GLU GLU ILE TYR SEQRES 11 A 279 PRO GLY ASP GLU GLU LYS SER LYS LEU PHE GLN ILE ILE SEQRES 12 A 279 GLU LEU LEU GLU GLU ALA PHE GLU ASP ALA VAL GLN LYS SEQRES 13 A 279 GLY PRO GLU ALA MET LYS THR LYS HIS VAL ILE LYS LEU SEQRES 14 A 279 ILE GLN ARG LYS ILE SER ASN SER ALA VAL LYS ASN ALA SEQRES 15 A 279 ASP LYS PRO LEU PRO ASN PRO ILE ALA ARG ILE ARG ILE SEQRES 16 A 279 LYS ILE ASN PRO ALA THR SER ILE LEU THR PRO ILE LEU SEQRES 17 A 279 LEU ASP LYS ASN LYS PRO ILE THR LEU GLN ASN GLY LYS SEQRES 18 A 279 THR SER PHE GLU GLU LEU LYS ASP GLU ASP GLY VAL LYS SEQRES 19 A 279 ALA ASN PRO ASP ASN ILE HIS LYS LEU ILE GLU SER HIS SEQRES 20 A 279 SER ILE HIS ASP GLY ILE ILE ASN ALA ARG SER ILE CYS SEQRES 21 A 279 ILE SER ASN MET GLY ILE SER PHE PRO LEU CYS LEU GLU SEQRES 22 A 279 MET GLY VAL VAL LYS VAL HET ACY A 301 7 HET ACY A 302 7 HET ACY A 303 7 HET ACY A 304 7 HETNAM ACY ACETIC ACID FORMUL 2 ACY 4(C2 H4 O2) FORMUL 6 HOH *155(H2 O) HELIX 1 AA1 HIS A 7 GLU A 21 1 15 HELIX 2 AA2 ASN A 23 SER A 26 5 4 HELIX 3 AA3 THR A 77 ASN A 88 1 12 HELIX 4 AA4 GLY A 132 LYS A 136 5 5 HELIX 5 AA5 SER A 137 LYS A 156 1 20 HELIX 6 AA6 PRO A 158 THR A 163 1 6 HELIX 7 AA7 ASN A 239 ILE A 244 1 6 SHEET 1 AA1 3 PHE A 28 ASP A 31 0 SHEET 2 AA1 3 LYS A 45 VAL A 53 -1 O ASN A 50 N SER A 29 SHEET 3 AA1 3 LYS A 56 PRO A 59 -1 O LYS A 56 N VAL A 53 SHEET 1 AA2 4 PHE A 28 ASP A 31 0 SHEET 2 AA2 4 LYS A 45 VAL A 53 -1 O ASN A 50 N SER A 29 SHEET 3 AA2 4 SER A 258 SER A 262 -1 O ILE A 261 N LYS A 45 SHEET 4 AA2 4 GLY A 265 SER A 267 -1 O SER A 267 N CYS A 260 SHEET 1 AA3 5 MET A 61 LYS A 68 0 SHEET 2 AA3 5 ILE A 249 ASN A 255 -1 O ILE A 254 N PHE A 62 SHEET 3 AA3 5 CYS A 271 LYS A 278 -1 O CYS A 271 N ASN A 255 SHEET 4 AA3 5 ILE A 207 THR A 216 1 N LYS A 211 O VAL A 277 SHEET 5 AA3 5 THR A 222 GLU A 226 -1 O SER A 223 N ILE A 215 SHEET 1 AA4 3 CYS A 101 ASN A 105 0 SHEET 2 AA4 3 ILE A 190 ARG A 194 -1 O ILE A 193 N LEU A 102 SHEET 3 AA4 3 ILE A 170 GLN A 171 -1 N GLN A 171 O ILE A 190 CRYST1 46.993 79.799 47.545 90.00 118.77 90.00 P 1 21 1 2 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 0.021280 0.000000 0.011683 0.00000 SCALE2 0.000000 0.012531 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023994 0.00000