PDB Short entry for 6XY4 HEADER APOPTOSIS 29-JAN-20 6XY4 TITLE STRUCTURAL INSIGHT INTO SHEEP-POX VIRUS MEDIATED INHIBITION OF TITLE 2 APOPTOSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTI-APOPTOTIC MEMBRANE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: ACTIVATOR OF APOPTOSIS HARAKIRI; COMPND 7 CHAIN: B; COMPND 8 SYNONYM: BH3-INTERACTING DOMAIN-CONTAINING PROTEIN 3,NEURONAL DEATH COMPND 9 PROTEIN DP5; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SHEEPPOX VIRUS (STRAIN TURKEY/TU-V02127); SOURCE 3 ORGANISM_TAXID: 654928; SOURCE 4 GENE: SPPV_14; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: C41; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS POX VIRUS, APOPTOSIS, BCL-2 EXPDTA X-RAY DIFFRACTION AUTHOR C.D.SURAWEERA,M.G.HINDS,M.KVANSAKUL REVDAT 2 24-JAN-24 6XY4 1 REMARK REVDAT 1 29-JUL-20 6XY4 0 JRNL AUTH C.D.SURAWEERA,D.R.BURTON,M.G.HINDS,M.KVANSAKUL JRNL TITL CRYSTAL STRUCTURES OF THE SHEEPPOX VIRUS ENCODED INHIBITOR JRNL TITL 2 OF APOPTOSIS SPPV14 BOUND TO THE PROAPOPTOTIC BH3 PEPTIDES JRNL TITL 3 HRK AND BAX. JRNL REF FEBS LETT. V. 594 2016 2020 JRNL REFN ISSN 0014-5793 JRNL PMID 32390192 JRNL DOI 10.1002/1873-3468.13807 REMARK 2 REMARK 2 RESOLUTION. 2.05 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.386 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 11236 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.055 REMARK 3 FREE R VALUE TEST SET COUNT : 568 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 31.0658 - 3.2473 0.98 2779 134 0.2041 0.2155 REMARK 3 2 3.2473 - 2.5778 0.99 2677 153 0.2366 0.2500 REMARK 3 3 2.5778 - 2.2521 0.99 2689 122 0.2398 0.2591 REMARK 3 4 2.2521 - 2.0462 0.95 2523 159 0.2574 0.2731 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) : 0.238 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.212 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 64.75 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 1245 REMARK 3 ANGLE : 0.398 1673 REMARK 3 CHIRALITY : 0.033 200 REMARK 3 PLANARITY : 0.001 211 REMARK 3 DIHEDRAL : 16.936 787 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): -18.4590 -12.5772 -11.1701 REMARK 3 T TENSOR REMARK 3 T11: 0.3569 T22: 0.3446 REMARK 3 T33: 0.3410 T12: 0.0201 REMARK 3 T13: 0.0175 T23: 0.0015 REMARK 3 L TENSOR REMARK 3 L11: 4.4534 L22: 2.5856 REMARK 3 L33: 4.6526 L12: 1.5391 REMARK 3 L13: 0.8234 L23: -0.8532 REMARK 3 S TENSOR REMARK 3 S11: -0.0565 S12: 0.3653 S13: 0.0211 REMARK 3 S21: -0.2790 S22: 0.1530 S23: 0.0900 REMARK 3 S31: 0.0813 S32: -0.0513 S33: 0.0042 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 6XY4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1292106501. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUL-19 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 : XDS 20180427 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 7.0 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11236 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.046 REMARK 200 RESOLUTION RANGE LOW (A) : 31.070 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 8.92 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 <I/SIGMA(I)> 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 1.11.1_2575-000 REMARK 200 STARTING MODEL: 2BJY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M POTASSIUM SODIUM TARTRATE REMARK 280 TETRAHYDRATE, 0.1 M BIS-TRIS PROPANE PH 6.5, 20% W/VPEG 3350, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 57.54000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 57.54000 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 1.000000 0.000000 0.000000 21.64000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.33000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 21.64000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.33000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 57.54000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 21.64000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 35.33000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 57.54000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 21.64000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 35.33000 REMARK 290 SMTRY3 8 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 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 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 ASP A 2 REMARK 465 ASN A 3 REMARK 465 CYS A 4 REMARK 465 VAL A 62 REMARK 465 ASP A 82 REMARK 465 PHE A 83 REMARK 465 GLU A 108 REMARK 465 VAL A 109 REMARK 465 VAL A 110 REMARK 465 LYS A 138 REMARK 465 LYS A 139 REMARK 465 LYS A 140 REMARK 465 ASN A 141 REMARK 465 LYS A 142 REMARK 465 GLN A 143 REMARK 465 ASN A 144 REMARK 465 ASP A 145 REMARK 465 ARG B 26 REMARK 465 ARG B 51 DBREF1 6XY4 A 1 145 UNP A0A3F2YKH3_SHEVT DBREF2 6XY4 A A0A3F2YKH3 1 145 DBREF 6XY4 B 26 51 UNP O00198 HRK_HUMAN 26 51 SEQADV 6XY4 GLY A -4 UNP A0A3F2YKH EXPRESSION TAG SEQADV 6XY4 PRO A -3 UNP A0A3F2YKH EXPRESSION TAG SEQADV 6XY4 LEU A -2 UNP A0A3F2YKH EXPRESSION TAG SEQADV 6XY4 GLY A -1 UNP A0A3F2YKH EXPRESSION TAG SEQADV 6XY4 SER A 0 UNP A0A3F2YKH EXPRESSION TAG SEQRES 1 A 150 GLY PRO LEU GLY SER MET ASP ASN CYS ASN TYR ASN ILE SEQRES 2 A 150 GLU LYS VAL LEU ASN VAL TYR LEU ARG ASP LEU ARG ILE SEQRES 3 A 150 GLU SER LEU ASN ASN ASN GLU LEU GLU ILE LEU ILE MET SEQRES 4 A 150 ILE ARG GLU CYS CYS GLU VAL ILE LYS LYS ASP TYR LYS SEQRES 5 A 150 THR GLU PHE ASN GLU ILE CYS ASN PHE ILE LEU GLN ASN SEQRES 6 A 150 ASN VAL LYS SER CYS TYR ASP ILE ASN ASP VAL LYS ASN SEQRES 7 A 150 ILE ILE ILE GLU THR ILE ASN SER ASP PHE ARG PRO SER SEQRES 8 A 150 VAL ILE LEU ALA SER ILE SER LEU LEU SER ILE ILE ILE SEQRES 9 A 150 LYS LYS LYS LYS ASP GLU ASN ASN GLU VAL VAL ASP ASP SEQRES 10 A 150 ASP LEU ALA LEU ASN GLU LEU ILE ASN LYS PHE SER SER SEQRES 11 A 150 TYR GLN LYS ASP ILE ILE SER PHE VAL GLU LYS ASN LYS SEQRES 12 A 150 LYS LYS ASN LYS GLN ASN ASP SEQRES 1 B 26 ARG SER SER ALA ALA GLN LEU THR ALA ALA ARG LEU LYS SEQRES 2 B 26 ALA LEU GLY ASP GLU LEU HIS GLN ARG THR MET TRP ARG FORMUL 3 HOH *28(H2 O) HELIX 1 AA1 ASN A 7 ASP A 18 1 12 HELIX 2 AA2 ARG A 20 LEU A 24 5 5 HELIX 3 AA3 ASN A 25 TYR A 46 1 22 HELIX 4 AA4 TYR A 46 LEU A 58 1 13 HELIX 5 AA5 ASP A 67 ASN A 80 1 14 HELIX 6 AA6 PRO A 85 ASN A 107 1 23 HELIX 7 AA7 ASP A 113 TYR A 126 1 14 HELIX 8 AA8 TYR A 126 LYS A 136 1 11 HELIX 9 AA9 SER B 28 TRP B 50 1 23 CRYST1 43.280 70.660 115.080 90.00 90.00 90.00 C 2 2 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 0.023105 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014152 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008690 0.00000