HEADER APOPTOSIS 16-JUN-17 5W60 TITLE CRYSTAL STRUCTURE OF BAXP168G MONOMER CRYO-PROTECTED WITH ETHYLENE TITLE 2 GLYCOL COMPND MOL_ID: 1; COMPND 2 MOLECULE: APOPTOSIS REGULATOR BAX; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BCL-2-LIKE PROTEIN 4,BCL2-L-4; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 OTHER_DETAILS: TWO ADDITIONAL SERINE RESIDUES AT C-TERMINUS DUE TO COMPND 8 CLONING STRATEGY. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: BAX, BCL2L4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BAX, INACTIVE MONOMER, APOPTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR A.Y.ROBIN,P.M.COLMAN,P.E.CZABOTAR REVDAT 5 04-OCT-23 5W60 1 REMARK REVDAT 4 17-OCT-18 5W60 1 JRNL REVDAT 3 05-SEP-18 5W60 1 JRNL REVDAT 2 29-AUG-18 5W60 1 JRNL REVDAT 1 27-JUN-18 5W60 0 JRNL AUTH A.Y.ROBIN,S.IYER,R.W.BIRKINSHAW,J.SANDOW,A.WARDAK,C.S.LUO, JRNL AUTH 2 M.SHI,A.I.WEBB,P.E.CZABOTAR,R.M.KLUCK,P.M.COLMAN JRNL TITL ENSEMBLE PROPERTIES OF BAX DETERMINE ITS FUNCTION. JRNL REF STRUCTURE V. 26 1346 2018 JRNL REFN ISSN 1878-4186 JRNL PMID 30122452 JRNL DOI 10.1016/J.STR.2018.07.006 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10_2152: ???) 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 13738 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 688 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 36.1810 - 3.0823 1.00 2735 144 0.1814 0.1937 REMARK 3 2 3.0823 - 2.4466 1.00 2611 138 0.1948 0.2717 REMARK 3 3 2.4466 - 2.1374 1.00 2586 136 0.1947 0.2686 REMARK 3 4 2.1374 - 1.9420 1.00 2557 135 0.2089 0.2808 REMARK 3 5 1.9420 - 1.8028 1.00 2561 135 0.2386 0.3209 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.360 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.006 1447 REMARK 3 ANGLE : 0.781 1969 REMARK 3 CHIRALITY : 0.044 224 REMARK 3 PLANARITY : 0.005 248 REMARK 3 DIHEDRAL : 12.606 859 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): -8.0742 -0.2681 10.3055 REMARK 3 T TENSOR REMARK 3 T11: 0.1112 T22: 0.1134 REMARK 3 T33: 0.1044 T12: 0.0312 REMARK 3 T13: 0.0146 T23: 0.0164 REMARK 3 L TENSOR REMARK 3 L11: 0.5915 L22: 0.6134 REMARK 3 L33: 0.9052 L12: -0.1017 REMARK 3 L13: -0.0937 L23: -0.0870 REMARK 3 S TENSOR REMARK 3 S11: -0.0012 S12: 0.0741 S13: 0.0220 REMARK 3 S21: -0.0536 S22: -0.0047 S23: -0.0432 REMARK 3 S31: -0.1098 S32: -0.1724 S33: -0.0207 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 5W60 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JUN-17. REMARK 100 THE DEPOSITION ID IS D_1000228423. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-SEP-13 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 : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13738 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.803 REMARK 200 RESOLUTION RANGE LOW (A) : 36.174 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.07706 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.82260 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: 4BD2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 26.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, TRIS, VAPOR REMARK 280 DIFFUSION, HANGING 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 21.85950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.20650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.35800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.20650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.85950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.35800 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL 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 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 MET A 1 REMARK 465 ASP A 2 REMARK 465 GLY A 3 REMARK 465 SER A 4 REMARK 465 GLY A 5 REMARK 465 GLU A 6 REMARK 465 GLN A 7 REMARK 465 PRO A 8 REMARK 465 ARG A 9 REMARK 465 GLY A 10 REMARK 465 LYS A 190 REMARK 465 MET A 191 REMARK 465 GLY A 192 REMARK 465 SER A 193 REMARK 465 SER A 194 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 ARG A 37 CG CD NE CZ NH1 NH2 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 VAL A 83 NZ LYS A 123 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 325 O HOH A 359 2454 2.17 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 GLU A 41 -66.84 -137.02 REMARK 500 LEU A 125 -19.30 -49.58 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 SO4 A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5W5X RELATED DB: PDB REMARK 900 RELATED ID: 5W5Z RELATED DB: PDB REMARK 900 RELATED ID: 5W61 RELATED DB: PDB REMARK 900 RELATED ID: 5W62 RELATED DB: PDB REMARK 900 RELATED ID: 5W63 RELATED DB: PDB DBREF 5W60 A 1 192 UNP Q07812 BAX_HUMAN 1 192 SEQADV 5W60 SER A 62 UNP Q07812 CYS 62 ENGINEERED MUTATION SEQADV 5W60 SER A 126 UNP Q07812 CYS 126 ENGINEERED MUTATION SEQADV 5W60 GLY A 168 UNP Q07812 PRO 168 ENGINEERED MUTATION SEQADV 5W60 SER A 193 UNP Q07812 EXPRESSION TAG SEQADV 5W60 SER A 194 UNP Q07812 EXPRESSION TAG SEQRES 1 A 194 MET ASP GLY SER GLY GLU GLN PRO ARG GLY GLY GLY PRO SEQRES 2 A 194 THR SER SER GLU GLN ILE MET LYS THR GLY ALA LEU LEU SEQRES 3 A 194 LEU GLN GLY PHE ILE GLN ASP ARG ALA GLY ARG MET GLY SEQRES 4 A 194 GLY GLU ALA PRO GLU LEU ALA LEU ASP PRO VAL PRO GLN SEQRES 5 A 194 ASP ALA SER THR LYS LYS LEU SER GLU SER LEU LYS ARG SEQRES 6 A 194 ILE GLY ASP GLU LEU ASP SER ASN MET GLU LEU GLN ARG SEQRES 7 A 194 MET ILE ALA ALA VAL ASP THR ASP SER PRO ARG GLU VAL SEQRES 8 A 194 PHE PHE ARG VAL ALA ALA ASP MET PHE SER ASP GLY ASN SEQRES 9 A 194 PHE ASN TRP GLY ARG VAL VAL ALA LEU PHE TYR PHE ALA SEQRES 10 A 194 SER LYS LEU VAL LEU LYS ALA LEU SER THR LYS VAL PRO SEQRES 11 A 194 GLU LEU ILE ARG THR ILE MET GLY TRP THR LEU ASP PHE SEQRES 12 A 194 LEU ARG GLU ARG LEU LEU GLY TRP ILE GLN ASP GLN GLY SEQRES 13 A 194 GLY TRP ASP GLY LEU LEU SER TYR PHE GLY THR GLY THR SEQRES 14 A 194 TRP GLN THR VAL THR ILE PHE VAL ALA GLY VAL LEU THR SEQRES 15 A 194 ALA SER LEU THR ILE TRP LYS LYS MET GLY SER SER HET SO4 A 201 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *96(H2 O) HELIX 1 AA1 SER A 15 ALA A 35 1 21 HELIX 2 AA2 ALA A 42 ALA A 46 5 5 HELIX 3 AA3 ASP A 53 SER A 72 1 20 HELIX 4 AA4 ASN A 73 ALA A 82 1 10 HELIX 5 AA5 PRO A 88 PHE A 100 1 13 HELIX 6 AA6 ASN A 106 ALA A 124 1 19 HELIX 7 AA7 LYS A 128 LEU A 148 1 21 HELIX 8 AA8 LEU A 148 GLN A 155 1 8 HELIX 9 AA9 GLY A 157 ASP A 159 5 3 HELIX 10 AB1 GLY A 160 GLY A 166 1 7 HELIX 11 AB2 THR A 169 TRP A 188 1 20 SITE 1 AC1 8 THR A 14 SER A 15 SER A 16 ARG A 89 SITE 2 AC1 8 TRP A 139 GLN A 153 HOH A 315 HOH A 329 CRYST1 43.719 50.716 64.413 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 0.022873 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019718 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015525 0.00000