HEADER APOPTOSIS 30-JUN-21 7P0S TITLE ORF VIRUS ENCODED BCL-2 HOMOLOG ORFV125 IN COMPLEX WITH PUMA BH3 TITLE 2 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: APOPTOSIS INHIBITOR; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: CONSERVED BCL-2 FOLD WITH 7 ALPHA HELICES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: BCL-2-BINDING COMPONENT 3, ISOFORMS 1/2; COMPND 8 CHAIN: U, C; COMPND 9 SYNONYM: JFY-1,P53 UP-REGULATED MODULATOR OF APOPTOSIS; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: PUMA BH3 PEPTIDE 26-MER 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; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606 KEYWDS ORF VIRUS, BCL-2, APOPTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR C.D.SURAWEERA,M.G.HINDS,M.KVANSAKUL REVDAT 3 31-JAN-24 7P0S 1 REMARK REVDAT 2 23-NOV-22 7P0S 1 JRNL REVDAT 1 13-JUL-22 7P0S 0 JRNL AUTH C.D.SURAWEERA,M.G.HINDS,M.KVANSAKUL JRNL TITL STRUCTURAL INVESTIGATION OF ORF VIRUS BCL-2 HOMOLOG ORFV125 JRNL TITL 2 INTERACTIONS WITH BH3-MOTIFS FROM BH3-ONLY PROTEINS PUMA AND JRNL TITL 3 HRK. JRNL REF VIRUSES V. 13 2021 JRNL REFN ESSN 1999-4915 JRNL PMID 34372579 JRNL DOI 10.3390/V13071374 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575_000 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.338 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 11017 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.247 REMARK 3 R VALUE (WORKING SET) : 0.245 REMARK 3 FREE R VALUE : 0.286 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.029 REMARK 3 FREE R VALUE TEST SET COUNT : 554 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 3.9727 - 3.1536 0.97 2608 123 0.2557 0.2782 REMARK 3 2 3.1536 - 2.7550 0.98 2602 142 0.3105 0.3449 REMARK 3 3 2.7550 - 2.5032 0.98 2580 134 0.3441 0.3946 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) : 0.431 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 36.192 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 62.96 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 : 0.002 2515 REMARK 3 ANGLE : 0.478 3405 REMARK 3 CHIRALITY : 0.032 382 REMARK 3 PLANARITY : 0.002 452 REMARK 3 DIHEDRAL : 19.805 1549 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): 21.6253 3.2890 5.7843 REMARK 3 T TENSOR REMARK 3 T11: 0.3842 T22: 0.3408 REMARK 3 T33: 0.4238 T12: 0.0419 REMARK 3 T13: 0.0092 T23: 0.0922 REMARK 3 L TENSOR REMARK 3 L11: 3.1304 L22: 4.2714 REMARK 3 L33: 2.6881 L12: 2.4507 REMARK 3 L13: 1.2566 L23: 1.7300 REMARK 3 S TENSOR REMARK 3 S11: 0.2008 S12: -0.1151 S13: -0.2365 REMARK 3 S21: 0.1347 S22: -0.1826 S23: -0.2678 REMARK 3 S31: -0.1541 S32: -0.0700 S33: 0.0084 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 7P0S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1292116247. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAR-20 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 : 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 7.0.078 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11059 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.503 REMARK 200 RESOLUTION RANGE LOW (A) : 43.283 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.09600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.9100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.35000 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: 7ADT REMARK 200 REMARK 200 REMARK: SINGLE ROD SHAPED CRYSTAL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM ACETATE, 25% PEG 3350, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 24.51650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.05850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.78200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.05850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.51650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.78200 REMARK 290 SMTRY3 4 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, U, B, C 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 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 ARG A 4 REMARK 465 ALA A 81 REMARK 465 THR A 143 REMARK 465 GLU U 130 REMARK 465 GLU U 131 REMARK 465 GLY B -4 REMARK 465 PRO B -3 REMARK 465 LEU B -2 REMARK 465 GLY B -1 REMARK 465 SER B 0 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 ASN B 3 REMARK 465 ARG B 4 REMARK 465 ARG B 62 REMARK 465 ALA B 63 REMARK 465 ASN B 64 REMARK 465 PRO B 65 REMARK 465 GLU B 66 REMARK 465 ALA B 81 REMARK 465 THR B 143 REMARK 465 GLU C 130 REMARK 465 GLU C 131 REMARK 465 GLN C 132 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 TRP B 102 73.26 -102.12 REMARK 500 REMARK 500 REMARK: NULL DBREF1 7P0S A 1 143 UNP A0A0R8HV90_ORFV DBREF2 7P0S A A0A0R8HV90 1 143 DBREF 7P0S U 130 155 UNP Q9BXH1 BBC3_HUMAN 130 155 DBREF1 7P0S B 1 143 UNP A0A0R8HV90_ORFV DBREF2 7P0S B A0A0R8HV90 1 143 DBREF 7P0S C 130 155 UNP Q9BXH1 BBC3_HUMAN 130 155 SEQADV 7P0S GLY A -4 UNP A0A0R8HV9 EXPRESSION TAG SEQADV 7P0S PRO A -3 UNP A0A0R8HV9 EXPRESSION TAG SEQADV 7P0S LEU A -2 UNP A0A0R8HV9 EXPRESSION TAG SEQADV 7P0S GLY A -1 UNP A0A0R8HV9 EXPRESSION TAG SEQADV 7P0S SER A 0 UNP A0A0R8HV9 EXPRESSION TAG SEQADV 7P0S GLY B -4 UNP A0A0R8HV9 EXPRESSION TAG SEQADV 7P0S PRO B -3 UNP A0A0R8HV9 EXPRESSION TAG SEQADV 7P0S LEU B -2 UNP A0A0R8HV9 EXPRESSION TAG SEQADV 7P0S GLY B -1 UNP A0A0R8HV9 EXPRESSION TAG SEQADV 7P0S SER B 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 SEQRES 1 U 26 GLU GLU GLN TRP ALA ARG GLU ILE GLY ALA GLN LEU ARG SEQRES 2 U 26 ARG MET ALA ASP ASP LEU ASN ALA GLN TYR GLU ARG ARG SEQRES 1 B 148 GLY PRO LEU GLY SER MET ALA ASN ARG ASP ASP ILE ASP SEQRES 2 B 148 ALA SER ALA VAL MET ALA ALA TYR LEU ALA ARG GLU TYR SEQRES 3 B 148 ALA GLU ALA VAL GLU GLU GLN LEU THR PRO ARG GLU ARG SEQRES 4 B 148 ASP ALA LEU GLU ALA LEU ARG VAL SER GLY GLU GLU VAL SEQRES 5 B 148 ARG SER PRO LEU LEU GLN GLU LEU SER ASN ALA GLY GLU SEQRES 6 B 148 HIS ARG ALA ASN PRO GLU ASN SER HIS ILE PRO ALA ALA SEQRES 7 B 148 LEU VAL SER ALA LEU LEU GLU ALA PRO THR SER PRO GLY SEQRES 8 B 148 ARG MET VAL THR ALA VAL GLU LEU CYS ALA GLN MET GLY SEQRES 9 B 148 ARG LEU TRP THR ARG GLY ARG GLN LEU VAL ASP PHE MET SEQRES 10 B 148 ARG LEU VAL TYR VAL LEU LEU ASP ARG LEU PRO PRO THR SEQRES 11 B 148 ALA ASP GLU ASP LEU GLY ALA TRP LEU GLN ALA VAL ALA SEQRES 12 B 148 ARG VAL HIS GLY THR SEQRES 1 C 26 GLU GLU GLN TRP ALA ARG GLU ILE GLY ALA GLN LEU ARG SEQRES 2 C 26 ARG MET ALA ASP ASP LEU ASN ALA GLN TYR GLU ARG ARG FORMUL 5 HOH *25(H2 O) HELIX 1 AA1 ASP A 8 LEU A 29 1 22 HELIX 2 AA2 THR A 30 GLY A 59 1 30 HELIX 3 AA3 GLY A 59 ASN A 64 1 6 HELIX 4 AA4 SER A 68 LEU A 79 1 12 HELIX 5 AA5 SER A 84 TRP A 102 1 19 HELIX 6 AA6 ARG A 106 ARG A 121 1 16 HELIX 7 AA7 THR A 125 GLY A 142 1 18 HELIX 8 AA8 TRP U 133 GLN U 151 1 19 HELIX 9 AA9 ASP B 8 GLN B 28 1 21 HELIX 10 AB1 THR B 30 ASN B 57 1 28 HELIX 11 AB2 SER B 68 LEU B 79 1 12 HELIX 12 AB3 SER B 84 TRP B 102 1 19 HELIX 13 AB4 ARG B 106 ARG B 121 1 16 HELIX 14 AB5 THR B 125 GLY B 142 1 18 HELIX 15 AB6 ALA C 134 ARG C 154 1 21 CRYST1 49.033 69.564 92.117 90.00 90.00 90.00 P 21 21 21 8 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 0.020394 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014375 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010856 0.00000