HEADER APOPTOSIS 28-NOV-19 6V4M TITLE TRICHURIS SUIS BCL-2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BCL-2; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRICHURIS SUIS; SOURCE 3 ORGANISM_COMMON: PIG WHIPWORM; SOURCE 4 ORGANISM_TAXID: 68888; SOURCE 5 GENE: M513_07322, M514_07322; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS BCL-2, HELICAL BUNDLE, APOPTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR W.D.FAIRLIE,E.F.LEE,B.J.SMITH REVDAT 2 11-OCT-23 6V4M 1 REMARK REVDAT 1 07-OCT-20 6V4M 0 JRNL AUTH N.D.YOUNG,T.J.HARRIS,M.EVANGELISTA,S.TRAN,M.A.WOUTERS, JRNL AUTH 2 T.P.SOARES DA COSTA,N.J.KERSHAW,R.B.GASSER,B.J.SMITH, JRNL AUTH 3 E.F.LEE,W.D.FAIRLIE JRNL TITL DIVERSITY IN THE INTRINSIC APOPTOSIS PATHWAY OF NEMATODES. JRNL REF COMMUN BIOL V. 3 478 2020 JRNL REFN ESSN 2399-3642 JRNL PMID 32859965 JRNL DOI 10.1038/S42003-020-01208-5 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11_2567 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 23576 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1179 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 3.9199 - 3.1969 1.00 3009 159 0.1541 0.1697 REMARK 3 2 3.1969 - 2.5376 1.00 2839 149 0.1845 0.1972 REMARK 3 3 2.5376 - 2.2169 1.00 2789 147 0.1638 0.2107 REMARK 3 4 2.2169 - 2.0142 1.00 2783 146 0.1623 0.1886 REMARK 3 5 2.0142 - 1.8698 1.00 2752 145 0.1721 0.2167 REMARK 3 6 1.8698 - 1.7596 1.00 2756 145 0.1758 0.1823 REMARK 3 7 1.7596 - 1.6715 1.00 2736 144 0.1856 0.1885 REMARK 3 8 1.6715 - 1.5990 1.00 2733 144 0.2165 0.2453 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.460 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.17 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 1361 REMARK 3 ANGLE : 0.774 1851 REMARK 3 CHIRALITY : 0.046 204 REMARK 3 PLANARITY : 0.005 232 REMARK 3 DIHEDRAL : 12.659 814 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): 36.4645 -5.4155 38.9164 REMARK 3 T TENSOR REMARK 3 T11: 0.0801 T22: 0.1179 REMARK 3 T33: 0.1027 T12: -0.0060 REMARK 3 T13: -0.0017 T23: 0.0018 REMARK 3 L TENSOR REMARK 3 L11: 1.1453 L22: 1.1668 REMARK 3 L33: 1.7896 L12: 0.0845 REMARK 3 L13: 0.4285 L23: 0.2686 REMARK 3 S TENSOR REMARK 3 S11: -0.0220 S12: 0.0840 S13: -0.0550 REMARK 3 S21: -0.0089 S22: 0.0123 S23: -0.0118 REMARK 3 S31: -0.0038 S32: 0.0980 S33: 0.0110 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 6V4M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-DEC-19. REMARK 100 THE DEPOSITION ID IS D_1000245737. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-NOV-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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 : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23576 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.599 REMARK 200 RESOLUTION RANGE LOW (A) : 39.199 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 14.10 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.1500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 14.20 REMARK 200 R MERGE FOR SHELL (I) : 0.76000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.940 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AUTO-RICKSHAW REMARK 200 STARTING MODEL: 3FDL CHAIN A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-CHLORIDE PH8.5, 0.2M LITHIUM REMARK 280 SULPHATE, 2M SODIUM CHLORIDE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 55.62450 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 27.62400 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 27.62400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 27.81225 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 27.62400 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 27.62400 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 83.43675 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 27.62400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 27.62400 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 27.81225 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 27.62400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 27.62400 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 83.43675 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 55.62450 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 425 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 -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 ALA A 3 REMARK 465 HIS A 4 REMARK 465 ASN A 5 REMARK 465 GLU A 169 REMARK 465 GLU A 170 REMARK 465 ASP A 171 REMARK 465 GLY A 172 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 14 CG CD OE1 NE2 REMARK 470 LYS A 62 CE NZ REMARK 470 LYS A 81 CB CG CD CE NZ REMARK 470 LYS A 158 CD CE NZ 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 ALA A 142 -38.46 -137.80 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 CL A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 304 DBREF1 6V4M A 1 172 UNP A0A085NFU1_9BILA DBREF2 6V4M A A0A085NFU1 1 172 SEQADV 6V4M GLY A -1 UNP A0A085NFU EXPRESSION TAG SEQADV 6V4M SER A 0 UNP A0A085NFU EXPRESSION TAG SEQRES 1 A 174 GLY SER MET SER ALA HIS ASN TRP ASP ASN GLU LEU SER SEQRES 2 A 174 GLY ILE GLN ASN THR SER VAL SER LEU ALA ALA ASP TYR SEQRES 3 A 174 VAL TYR MET ARG LEU ALA THR GLU GLY PHE VAL PHE GLY SEQRES 4 A 174 ILE ARG SER SER VAL ARG ALA PRO ILE ARG LEU CYS ASP SEQRES 5 A 174 ALA MET PHE LEU MET CYS ASP LEU PHE GLU ARG LYS PHE SEQRES 6 A 174 HIS ASP ARG TYR ILE ALA PRO LEU LYS ASN ALA CYS LEU SEQRES 7 A 174 GLY ILE SER ALA LYS ASP MET ASP MET ARG MET PHE PHE SEQRES 8 A 174 SER ALA LEU ASP SER VAL PHE SER SER GLY ILE SER TRP SEQRES 9 A 174 SER ARG ILE VAL ALA MET TYR ALA PHE ALA GLY SER VAL SEQRES 10 A 174 ALA LEU ALA CYS ALA ARG GLN GLY ARG ARG GLN THR VAL SEQRES 11 A 174 ILE ALA ILE PRO GLU TRP ILE MET LEU TYR MET ARG ARG SEQRES 12 A 174 ALA ILE ALA PRO TRP ILE HIS ALA ASN GLY GLY TRP ASP SEQRES 13 A 174 SER PHE ILE LYS PHE SER GLN ASP VAL LEU ASN GLY ASN SEQRES 14 A 174 HIS GLU GLU ASP GLY HET CL A 301 1 HET CL A 302 1 HET CL A 303 1 HET SO4 A 304 5 HETNAM CL CHLORIDE ION HETNAM SO4 SULFATE ION FORMUL 2 CL 3(CL 1-) FORMUL 5 SO4 O4 S 2- FORMUL 6 HOH *121(H2 O) HELIX 1 AA1 ASN A 8 GLU A 32 1 25 HELIX 2 AA2 PRO A 45 PHE A 63 1 19 HELIX 3 AA3 PHE A 63 ILE A 68 1 6 HELIX 4 AA4 ILE A 68 CYS A 75 1 8 HELIX 5 AA5 SER A 79 MET A 83 5 5 HELIX 6 AA6 ASP A 84 SER A 97 1 14 HELIX 7 AA7 SER A 101 GLN A 122 1 22 HELIX 8 AA8 ARG A 124 ARG A 140 1 17 HELIX 9 AA9 ALA A 142 ASN A 150 1 9 HELIX 10 AB1 GLY A 151 GLY A 166 1 16 SITE 1 AC1 5 TYR A 26 ILE A 38 ARG A 39 HOH A 446 SITE 2 AC1 5 HOH A 456 SITE 1 AC2 2 ASN A 8 GLU A 9 SITE 1 AC3 3 GLU A 32 GLY A 33 TRP A 146 SITE 1 AC4 5 LYS A 72 MET A 83 PHE A 111 SER A 114 SITE 2 AC4 5 VAL A 115 CRYST1 55.248 55.248 111.249 90.00 90.00 90.00 P 41 21 2 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 0.018100 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018100 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008989 0.00000