HEADER APOPTOSIS 17-JAN-22 7QTW TITLE KAPOSI SARCOMA ASSOCIATED HERPES VIRUS(KSHV) ENCODED APOPTOSIS TITLE 2 INHIBITOR, KSBCL-2 IN COMPLEX WITH BID BH3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BCL-2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ORF 16,ORF16,ORF16 PROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: BH3-INTERACTING DOMAIN DEATH AGONIST P15; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: P15 BID; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN GAMMAHERPESVIRUS 8; SOURCE 3 ORGANISM_TAXID: 37296; SOURCE 4 GENE: ORF16, HHV8GK18_GP19; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: CODON PLUS (RIL); 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 APOPTOSIS, VIRAL BCL-2 PROTEIN, GAMMA HERPES VIRUS, KAPOSI SARCOMA KEYWDS 2 VIRUS EXPDTA X-RAY DIFFRACTION AUTHOR C.D.SURAWEERA,M.G.HINDS,M.KVANSAKUL REVDAT 1 23-NOV-22 7QTW 0 JRNL AUTH C.D.SURAWEERA,M.G.HINDS,M.KVANSAKUL JRNL TITL STRUCTURAL INSIGHT INTO KSBCL-2 MEDIATED APOPTOSIS JRNL TITL 2 INHIBITION BY KAPOSI SARCOMA ASSOCIATED HERPES VIRUS. JRNL REF VIRUSES V. 14 2022 JRNL REFN ESSN 1999-4915 JRNL PMID 35458468 JRNL DOI 10.3390/V14040738 REMARK 2 REMARK 2 RESOLUTION. 1.41 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 1.41 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.74 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.420 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 44712 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 2256 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 3.5500 - 2.8200 1.00 2668 170 0.1610 0.1813 REMARK 3 2 2.8200 - 2.4600 1.00 2681 152 0.1577 0.1865 REMARK 3 3 2.4600 - 2.2400 1.00 2658 140 0.1695 0.2352 REMARK 3 4 2.2400 - 2.0800 1.00 2684 148 0.1469 0.1811 REMARK 3 5 2.0800 - 1.9600 1.00 2682 113 0.1733 0.1847 REMARK 3 6 1.9600 - 1.8600 1.00 2661 138 0.1807 0.2583 REMARK 3 7 1.8600 - 1.7800 1.00 2645 149 0.2189 0.2872 REMARK 3 8 1.7800 - 1.7100 1.00 2655 139 0.2289 0.2528 REMARK 3 9 1.7100 - 1.6500 1.00 2672 130 0.2589 0.3302 REMARK 3 10 1.6500 - 1.6000 1.00 2644 137 0.2678 0.3219 REMARK 3 11 1.6000 - 1.5500 1.00 2667 138 0.2940 0.3639 REMARK 3 12 1.5500 - 1.5100 1.00 2671 117 0.3055 0.3696 REMARK 3 13 1.5100 - 1.4700 0.99 2636 148 0.3262 0.3720 REMARK 3 14 1.4700 - 1.4400 0.98 2564 169 0.3450 0.3962 REMARK 3 15 1.4400 - 1.4100 0.95 2536 112 0.3576 0.4535 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.370 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.09 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.86 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 : 0.014 1399 REMARK 3 ANGLE : 1.132 1887 REMARK 3 CHIRALITY : 0.081 205 REMARK 3 PLANARITY : 0.011 245 REMARK 3 DIHEDRAL : 12.363 513 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 7QTW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-JAN-22. REMARK 100 THE DEPOSITION ID IS D_1292120283. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAR-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 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 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44937 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.410 REMARK 200 RESOLUTION RANGE LOW (A) : 38.740 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 19.30 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.41 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.46 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 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: ALPHA FOLD GENERATED MODEL FOR THIS PROTEIN REMARK 200 SEQUENCE REMARK 200 REMARK 200 REMARK: LARGE SINGLE HEXAGONAL CRYSTAL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE PH 4.6 8% PEG REMARK 280 4000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,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 17.01867 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 34.03733 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 17.01867 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 34.03733 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: 2580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 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 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 HOH A 408 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 SER B 79 REMARK 465 LEU B 108 REMARK 465 VAL B 109 REMARK 465 ASN B 110 REMARK 465 GLY B 111 REMARK 465 LEU B 112 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 383 O HOH A 388 2.15 REMARK 500 REMARK 500 REMARK: NULL 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 ASP A 2 52.57 -103.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 431 DISTANCE = 6.06 ANGSTROMS DBREF 7QTW A 1 146 UNP Q76RI8 Q76RI8_HHV8 1 146 DBREF 7QTW B 79 112 UNP P55957 BID_HUMAN 76 109 SEQADV 7QTW GLY A -4 UNP Q76RI8 EXPRESSION TAG SEQADV 7QTW PRO A -3 UNP Q76RI8 EXPRESSION TAG SEQADV 7QTW LEU A -2 UNP Q76RI8 EXPRESSION TAG SEQADV 7QTW GLY A -1 UNP Q76RI8 EXPRESSION TAG SEQADV 7QTW SER A 0 UNP Q76RI8 EXPRESSION TAG SEQADV 7QTW ALA A 117 UNP Q76RI8 VAL 117 ENGINEERED MUTATION SEQRES 1 A 151 GLY PRO LEU GLY SER MET ASP GLU ASP VAL LEU PRO GLY SEQRES 2 A 151 GLU VAL LEU ALA ILE GLU GLY ILE PHE MET ALA CYS GLY SEQRES 3 A 151 LEU ASN GLU PRO GLU TYR LEU TYR HIS PRO LEU LEU SER SEQRES 4 A 151 PRO ILE LYS LEU TYR ILE THR GLY LEU MET ARG ASP LYS SEQRES 5 A 151 GLU SER LEU PHE GLU ALA MET LEU ALA ASN VAL ARG PHE SEQRES 6 A 151 HIS SER THR THR GLY ILE ASN GLN LEU GLY LEU SER MET SEQRES 7 A 151 LEU GLN VAL SER GLY ASP GLY ASN MET ASN TRP GLY ARG SEQRES 8 A 151 ALA LEU ALA ILE LEU THR PHE GLY SER PHE VAL ALA GLN SEQRES 9 A 151 LYS LEU SER ASN GLU PRO HIS LEU ARG ASP PHE ALA LEU SEQRES 10 A 151 ALA VAL LEU PRO ALA TYR ALA TYR GLU ALA ILE GLY PRO SEQRES 11 A 151 GLN TRP PHE ARG ALA ARG GLY GLY TRP ARG GLY LEU LYS SEQRES 12 A 151 ALA TYR CYS THR GLN VAL LEU THR SEQRES 1 B 34 SER GLU SER GLN GLU ASP ILE ILE ARG ASN ILE ALA ARG SEQRES 2 B 34 HIS LEU ALA GLN VAL GLY ASP SER MET ASP ARG SER ILE SEQRES 3 B 34 PRO PRO GLY LEU VAL ASN GLY LEU HET EDO A 201 10 HET EDO A 202 10 HET EDO A 203 10 HET EDO A 204 10 HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 EDO 4(C2 H6 O2) FORMUL 7 HOH *148(H2 O) HELIX 1 AA1 VAL A 5 ASN A 23 1 19 HELIX 2 AA2 HIS A 30 LEU A 32 5 3 HELIX 3 AA3 LEU A 33 LYS A 47 1 15 HELIX 4 AA4 LYS A 47 LEU A 55 1 9 HELIX 5 AA5 SER A 62 VAL A 76 1 15 HELIX 6 AA6 SER A 77 GLY A 80 5 4 HELIX 7 AA7 ASN A 83 LEU A 101 1 19 HELIX 8 AA8 GLU A 104 GLY A 124 1 21 HELIX 9 AA9 GLY A 124 ALA A 130 1 7 HELIX 10 AB1 GLY A 132 VAL A 144 1 13 HELIX 11 AB2 SER B 81 ASP B 101 1 21 CRYST1 89.476 89.476 51.056 90.00 90.00 120.00 P 64 6 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 0.011176 0.006453 0.000000 0.00000 SCALE2 0.000000 0.012905 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019586 0.00000