HEADER APOPTOSIS 16-SEP-20 7ADS TITLE ORF VIRUS APOPTOSIS INHIBITOR ORFV125 COMPND MOL_ID: 1; COMPND 2 MOLECULE: APOPTOSIS INHIBITOR; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ORF VIRUS; SOURCE 3 ORGANISM_COMMON: ORFV; SOURCE 4 ORGANISM_TAXID: 10258; SOURCE 5 GENE: ORFV125, ORF125; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: C41 KEYWDS ORF VIRUS, APOPTOSIS, BCL-2, ITC EXPDTA X-RAY DIFFRACTION AUTHOR C.D.SURAWEERA,M.G.HINDS,M.KVANSAKUL REVDAT 3 01-MAY-24 7ADS 1 REMARK REVDAT 2 23-NOV-22 7ADS 1 JRNL REMARK REVDAT 1 06-OCT-21 7ADS 0 JRNL AUTH C.D.SURAWEERA,M.G.HINDS,M.KVANSAKUL JRNL TITL CRYSTAL STRUCTURES OF ORFV125 PROVIDE INSIGHT INTO ORF JRNL TITL 2 VIRUS-MEDIATED INHIBITION OF APOPTOSIS. JRNL REF BIOCHEM.J. V. 477 4527 2020 JRNL REFN ESSN 1470-8728 JRNL PMID 33175095 JRNL DOI 10.1042/BCJ20200776 REMARK 2 REMARK 2 RESOLUTION. 2.22 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.22 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.344 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 10471 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.245 REMARK 3 R VALUE (WORKING SET) : 0.244 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.224 REMARK 3 FREE R VALUE TEST SET COUNT : 547 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 3.5242 - 3.5242 1.00 2603 162 0.2226 0.2265 REMARK 3 2 3.5242 - 2.7973 1.00 2477 122 0.2665 0.3135 REMARK 3 3 2.7973 - 2.4438 1.00 2429 136 0.2788 0.3242 REMARK 3 4 2.4438 - 2.2203 1.00 2415 127 0.3205 0.3795 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) : 0.254 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.392 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 54.15 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 70.00 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 : 0.003 1079 REMARK 3 ANGLE : 0.540 1450 REMARK 3 CHIRALITY : 0.034 166 REMARK 3 PLANARITY : 0.004 190 REMARK 3 DIHEDRAL : 21.764 661 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): 9.4090 41.0463 -1.1337 REMARK 3 T TENSOR REMARK 3 T11: 0.3017 T22: 0.5514 REMARK 3 T33: 0.4150 T12: 0.0108 REMARK 3 T13: 0.0547 T23: 0.0504 REMARK 3 L TENSOR REMARK 3 L11: 3.7050 L22: 1.9576 REMARK 3 L33: 1.4627 L12: 0.0242 REMARK 3 L13: -0.4188 L23: 0.4937 REMARK 3 S TENSOR REMARK 3 S11: 0.0517 S12: -0.1134 S13: -0.1146 REMARK 3 S21: 0.0191 S22: -0.0850 S23: 0.0816 REMARK 3 S31: 0.1034 S32: -0.2999 S33: -0.0137 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 7ADS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-SEP-20. REMARK 100 THE DEPOSITION ID IS D_1292111248. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUL-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10487 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.220 REMARK 200 RESOLUTION RANGE LOW (A) : 50.660 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 19.20 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.22 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.29 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.10000 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: ORFV_BAX REMARK 200 REMARK 200 REMARK: THICK DIAMOND SHAPE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M SODIUM CITRATE TRIBASIC DEHYDRATE REMARK 280 0.02M MAGNESIUM CHLORIDE 0.1M BIS TRIS PROPANE 20% PEG 3350, PH REMARK 280 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+2/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-Z+1/3 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 40.39267 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 20.19633 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 0.00000 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 40.39267 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 20.19633 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 40.39267 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 20.19633 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 40.39267 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 0.00000 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 20.19633 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: 8820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -147.0 KCAL/MOL 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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 NA NA A 310 LIES ON A SPECIAL POSITION. REMARK 375 MG MG A 318 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 421 LIES ON A SPECIAL POSITION. 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 GLY A -4 REMARK 465 PRO A -3 REMARK 465 LEU A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 ASN A 3 REMARK 465 HIS A 61 REMARK 465 ARG A 62 REMARK 465 ALA A 63 REMARK 465 ALA A 81 REMARK 465 THR A 143 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 310 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 49 OG REMARK 620 2 SER A 49 OG 0.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 311 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 79 O REMARK 620 2 ARG A 121 O 97.1 REMARK 620 N 1 DBREF1 7ADS A 1 143 UNP A0A0R8HV90_ORFV DBREF2 7ADS A A0A0R8HV90 1 143 SEQADV 7ADS GLY A -4 UNP A0A0R8HV9 EXPRESSION TAG SEQADV 7ADS PRO A -3 UNP A0A0R8HV9 EXPRESSION TAG SEQADV 7ADS LEU A -2 UNP A0A0R8HV9 EXPRESSION TAG SEQADV 7ADS GLY A -1 UNP A0A0R8HV9 EXPRESSION TAG SEQADV 7ADS SER A 0 UNP A0A0R8HV9 EXPRESSION TAG SEQRES 1 A 148 GLY PRO LEU GLY SER MET ALA ASN ARG ASP ASP ILE ASP SEQRES 2 A 148 ALA SER ALA VAL MET ALA ALA TYR LEU ALA ARG GLU TYR SEQRES 3 A 148 ALA GLU ALA VAL GLU GLU GLN LEU THR PRO ARG GLU ARG SEQRES 4 A 148 ASP ALA LEU GLU ALA LEU ARG VAL SER GLY GLU GLU VAL SEQRES 5 A 148 ARG SER PRO LEU LEU GLN GLU LEU SER ASN ALA GLY GLU SEQRES 6 A 148 HIS ARG ALA ASN PRO GLU ASN SER HIS ILE PRO ALA ALA SEQRES 7 A 148 LEU VAL SER ALA LEU LEU GLU ALA PRO THR SER PRO GLY SEQRES 8 A 148 ARG MET VAL THR ALA VAL GLU LEU CYS ALA GLN MET GLY SEQRES 9 A 148 ARG LEU TRP THR ARG GLY ARG GLN LEU VAL ASP PHE MET SEQRES 10 A 148 ARG LEU VAL TYR VAL LEU LEU ASP ARG LEU PRO PRO THR SEQRES 11 A 148 ALA ASP GLU ASP LEU GLY ALA TRP LEU GLN ALA VAL ALA SEQRES 12 A 148 ARG VAL HIS GLY THR HET EDO A 301 10 HET EDO A 302 10 HET EDO A 303 10 HET EDO A 304 10 HET EDO A 305 10 HET EDO A 306 10 HET EDO A 307 10 HET NA A 308 1 HET NA A 309 1 HET NA A 310 1 HET NA A 311 1 HET NA A 312 1 HET CL A 313 1 HET CL A 314 1 HET MG A 315 1 HET MG A 316 1 HET MG A 317 1 HET MG A 318 1 HETNAM EDO 1,2-ETHANEDIOL HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM MG MAGNESIUM ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO 7(C2 H6 O2) FORMUL 9 NA 5(NA 1+) FORMUL 14 CL 2(CL 1-) FORMUL 16 MG 4(MG 2+) FORMUL 20 HOH *27(H2 O) HELIX 1 AA1 ASP A 8 LEU A 29 1 22 HELIX 2 AA2 THR A 30 GLU A 45 1 16 HELIX 3 AA3 SER A 49 ALA A 58 1 10 HELIX 4 AA4 GLU A 66 SER A 68 5 3 HELIX 5 AA5 HIS A 69 GLU A 80 1 12 HELIX 6 AA6 SER A 84 TRP A 102 1 19 HELIX 7 AA7 ARG A 104 ARG A 106 5 3 HELIX 8 AA8 GLN A 107 ARG A 121 1 15 HELIX 9 AA9 THR A 125 GLY A 142 1 18 LINK O GLN A 28 MG MG A 315 1555 1555 2.99 LINK OG SER A 49 NA NA A 310 1555 1555 2.90 LINK OG SER A 49 NA NA A 310 1555 7554 2.90 LINK O LEU A 79 NA NA A 311 1555 1555 2.75 LINK O ARG A 121 NA NA A 311 1555 1555 2.77 LINK NA NA A 309 O HOH A 404 1555 1555 2.69 CRYST1 106.613 106.613 60.589 90.00 90.00 120.00 P 62 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 0.009380 0.005415 0.000000 0.00000 SCALE2 0.000000 0.010831 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016505 0.00000