HEADER APOPTOSIS 17-DEC-19 6TQP TITLE STRUCTURAL INSIGHT INTO TANAPOXVIRUS MEDIATED INHIBITION OF APOPTOSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: 16L PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: TANAPOX VIRUS BCL-2 HOMOLOGE; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: BCL-2-BINDING COMPONENT 3, ISOFORMS 1/2; COMPND 8 CHAIN: B; COMPND 9 SYNONYM: JFY-1,P53 UP-REGULATED MODULATOR OF APOPTOSIS; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: PUMA BH3 MOTIF (26-MER) SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: YABA-LIKE DISEASE VIRUS; SOURCE 3 ORGANISM_TAXID: 132475; SOURCE 4 GENE: 16L; 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 3 01-MAY-24 6TQP 1 REMARK REVDAT 2 16-DEC-20 6TQP 1 JRNL REVDAT 1 03-JUN-20 6TQP 0 JRNL AUTH C.D.SURAWEERA,M.I.ANASIR,S.CHUGH,A.JAVORSKY,R.E.IMPEY, JRNL AUTH 2 M.HASAN ZADEH,T.P.SOARES DA COSTA,M.G.HINDS,M.KVANSAKUL JRNL TITL STRUCTURAL INSIGHT INTO TANAPOXVIRUS-MEDIATED INHIBITION OF JRNL TITL 2 APOPTOSIS. JRNL REF FEBS J. V. 287 3733 2020 JRNL REFN ISSN 1742-464X JRNL PMID 32412687 JRNL DOI 10.1111/FEBS.15365 REMARK 2 REMARK 2 RESOLUTION. 1.85 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.338 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 15799 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.823 REMARK 3 FREE R VALUE TEST SET COUNT : 762 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 32.4500 - 3.1617 1.00 3139 162 0.1739 0.2000 REMARK 3 2 3.1617 - 2.5098 1.00 3025 138 0.2013 0.2093 REMARK 3 3 2.5098 - 2.1926 1.00 2972 164 0.1837 0.2481 REMARK 3 4 2.1926 - 1.9922 1.00 2969 145 0.2257 0.2297 REMARK 3 5 1.9922 - 1.8494 0.99 2932 153 0.3038 0.3779 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) : 0.297 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.019 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.76 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.76 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 : 0.006 1383 REMARK 3 ANGLE : 0.687 1854 REMARK 3 CHIRALITY : 0.041 211 REMARK 3 PLANARITY : 0.004 238 REMARK 3 DIHEDRAL : 12.168 878 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): 36.5450 30.7032 18.4936 REMARK 3 T TENSOR REMARK 3 T11: 0.2651 T22: 0.2319 REMARK 3 T33: 0.2404 T12: -0.0061 REMARK 3 T13: 0.0306 T23: -0.0286 REMARK 3 L TENSOR REMARK 3 L11: 2.8235 L22: 2.4765 REMARK 3 L33: 3.0045 L12: -0.7337 REMARK 3 L13: 1.2762 L23: -0.6798 REMARK 3 S TENSOR REMARK 3 S11: 0.0064 S12: 0.0408 S13: 0.1327 REMARK 3 S21: 0.0626 S22: -0.0468 S23: -0.0474 REMARK 3 S31: -0.0563 S32: 0.0819 S33: 0.0380 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 6TQP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-DEC-19. REMARK 100 THE DEPOSITION ID IS D_1292105916. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-SEP-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 1.11.1_2575 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 7.0.077 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15799 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.849 REMARK 200 RESOLUTION RANGE LOW (A) : 32.450 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.89 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.07200 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: PREVIOUSLY SOLVED STRUCTURE OF TNP_16L REMARK 200 REMARK 200 REMARK: LONG ROD SHAPE CRYSTALS WITH SHARP EDGES REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M POTASSIUM THIOCYANATE, 30% PEG REMARK 280 2000MME, PH 7.5, 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 27.04650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.11000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.43450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.11000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.04650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.43450 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 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 GLU A 2 REMARK 465 GLN A 145 REMARK 465 LYS A 146 REMARK 465 SER A 147 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 366 O HOH B 216 2.18 REMARK 500 OD1 ASP A 79 O HOH A 301 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 201 DBREF 6TQP A 1 147 UNP Q9DHU6 Q9DHU6_YLDV 1 147 DBREF 6TQP B 129 154 UNP Q9BXH1 BBC3_HUMAN 130 155 SEQADV 6TQP GLY A -4 UNP Q9DHU6 EXPRESSION TAG SEQADV 6TQP PRO A -3 UNP Q9DHU6 EXPRESSION TAG SEQADV 6TQP LEU A -2 UNP Q9DHU6 EXPRESSION TAG SEQADV 6TQP GLY A -1 UNP Q9DHU6 EXPRESSION TAG SEQADV 6TQP SER A 0 UNP Q9DHU6 EXPRESSION TAG SEQRES 1 A 152 GLY PRO LEU GLY SER MET GLU ASN SER CYS ASN PHE ASN SEQRES 2 A 152 ASN SER ILE LYS ASN VAL ILE VAL PHE TYR ILE ASN GLU SEQRES 3 A 152 LYS ALA LEU ILE GLU GLU LYS LYS MET LEU SER CYS TYR SEQRES 4 A 152 GLU ASN LYS LEU LEU ASN LEU ILE LYS GLU ASP CYS GLU SEQRES 5 A 152 ASN ILE MET LEU LYS TYR LYS PRO ASN LEU SER TYR ILE SEQRES 6 A 152 CYS SER LEU LEU LYS VAL ASP ASP THR SER GLU GLU ASN SEQRES 7 A 152 ILE LYS HIS ILE LYS ASP GLN ILE ILE GLU SER LEU GLU SEQRES 8 A 152 ASN ASP ASN ARG PRO SER VAL LYS LEU ALA ILE ILE SER SEQRES 9 A 152 LEU ILE SER MET ILE VAL GLU MET ASN GLY TYR LYS GLY SEQRES 10 A 152 LYS ASN ILE PRO MET SER PHE LEU ILE GLU ASP ILE ALA SEQRES 11 A 152 LEU LYS ILE SER GLU ASN SER GLU ASP LEU ILE ASN PHE SEQRES 12 A 152 ILE ASN ILE LYS ASN LYS GLN LYS SER SEQRES 1 B 26 GLU GLU GLN TRP ALA ARG GLU ILE GLY ALA GLN LEU ARG SEQRES 2 B 26 ARG MET ALA ASP ASP LEU ASN ALA GLN TYR GLU ARG ARG HET NA A 201 1 HETNAM NA SODIUM ION FORMUL 3 NA NA 1+ FORMUL 4 HOH *91(H2 O) HELIX 1 AA1 ASN A 6 ALA A 23 1 18 HELIX 2 AA2 SER A 32 LEU A 64 1 33 HELIX 3 AA3 SER A 70 ASP A 88 1 19 HELIX 4 AA4 ARG A 90 GLY A 109 1 20 HELIX 5 AA5 ASN A 114 GLU A 130 1 17 HELIX 6 AA6 ASN A 131 LYS A 144 1 14 HELIX 7 AA7 TRP B 132 ARG B 154 1 23 LINK OE1 GLU A 71 NA NA A 201 1555 1555 2.41 SITE 1 AC1 1 GLU A 71 CRYST1 54.093 54.869 60.220 90.00 90.00 90.00 P 21 21 21 4 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 0.018487 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018225 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016606 0.00000