HEADER APOPTOSIS 16-JUN-17 5W62 TITLE CRYSTAL STRUCTURE OF MOUSE BAX MONOMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: APOPTOSIS REGULATOR BAX; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: BAX; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BAX, MONOMER, MOUSE, APOPTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR A.Y.ROBIN,P.M.COLMAN,P.E.CZABOTAR,C.S.LUO REVDAT 5 04-OCT-23 5W62 1 REMARK REVDAT 4 17-OCT-18 5W62 1 JRNL REVDAT 3 05-SEP-18 5W62 1 JRNL REVDAT 2 29-AUG-18 5W62 1 JRNL REVDAT 1 27-JUN-18 5W62 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. 2.20 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.24 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 7218 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 722 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 34.2398 - 3.7541 1.00 1372 154 0.1912 0.2474 REMARK 3 2 3.7541 - 2.9803 1.00 1310 145 0.2058 0.3133 REMARK 3 3 2.9803 - 2.6037 1.00 1272 140 0.2350 0.3267 REMARK 3 4 2.6037 - 2.3657 1.00 1274 142 0.2414 0.3302 REMARK 3 5 2.3657 - 2.1962 1.00 1268 141 0.2459 0.3194 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) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.290 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 1236 REMARK 3 ANGLE : 0.747 1677 REMARK 3 CHIRALITY : 0.043 193 REMARK 3 PLANARITY : 0.005 206 REMARK 3 DIHEDRAL : 10.999 710 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): -12.1366 -0.6044 -13.1954 REMARK 3 T TENSOR REMARK 3 T11: 0.2872 T22: 0.2730 REMARK 3 T33: 0.2873 T12: -0.0409 REMARK 3 T13: -0.0306 T23: -0.0087 REMARK 3 L TENSOR REMARK 3 L11: 1.7039 L22: 2.6925 REMARK 3 L33: 2.8669 L12: -0.8979 REMARK 3 L13: 0.2803 L23: -1.6853 REMARK 3 S TENSOR REMARK 3 S11: 0.1709 S12: -0.0931 S13: 0.0295 REMARK 3 S21: -0.1430 S22: 0.0827 S23: 0.1795 REMARK 3 S31: 0.1424 S32: 0.0008 S33: 0.0044 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 5W62 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_1000228427. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-NOV-14 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 : 7218 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.196 REMARK 200 RESOLUTION RANGE LOW (A) : 34.236 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.06850 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.4400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 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) : 0.97650 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, 5W60 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 21.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.56 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 20.39350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.49250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.97500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.49250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.39350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.97500 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: 90 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 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 LEU A 8 REMARK 465 GLY A 9 REMARK 465 SER A 10 REMARK 465 GLY A 11 REMARK 465 GLY A 12 REMARK 465 GLY A 36 REMARK 465 ARG A 37 REMARK 465 MET A 38 REMARK 465 ALA A 39 REMARK 465 GLY A 40 REMARK 465 GLU A 41 REMARK 465 THR A 42 REMARK 465 PRO A 43 REMARK 465 GLU A 44 REMARK 465 LEU A 45 REMARK 465 THR A 46 REMARK 465 LEU A 47 REMARK 465 GLU A 48 REMARK 465 GLN A 49 REMARK 465 PRO A 50 REMARK 465 PRO A 51 REMARK 465 GLN A 52 REMARK 465 SER A 126 REMARK 465 THR A 127 REMARK 465 LYS A 128 REMARK 465 VAL A 129 REMARK 465 LYS A 190 REMARK 465 MET A 191 REMARK 465 GLY A 192 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 ASP A 53 CG OD1 OD2 REMARK 470 LYS A 58 CG CD CE NZ REMARK 470 THR A 85 OG1 CG2 REMARK 470 ASP A 86 CG OD1 OD2 REMARK 470 SER A 87 OG REMARK 470 ARG A 89 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 90 CG CD OE1 OE2 REMARK 470 LEU A 125 CG CD1 CD2 REMARK 470 ARG A 145 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 146 CG CD OE1 OE2 REMARK 470 GLU A 159 CG CD OE1 OE2 REMARK 470 LYS A 189 CG 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 ASP A 82 46.85 -81.57 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: 5W60 RELATED DB: PDB REMARK 900 RELATED ID: 5W61 RELATED DB: PDB REMARK 900 RELATED ID: 5W63 RELATED DB: PDB DBREF 5W62 A 1 192 UNP Q07813 BAX_MOUSE 1 192 SEQADV 5W62 SER A 62 UNP Q07813 CYS 62 ENGINEERED MUTATION SEQADV 5W62 SER A 126 UNP Q07813 CYS 126 ENGINEERED MUTATION SEQRES 1 A 192 MET ASP GLY SER GLY GLU GLN LEU GLY SER GLY GLY PRO SEQRES 2 A 192 THR SER SER GLU GLN ILE MET LYS THR GLY ALA PHE LEU SEQRES 3 A 192 LEU GLN GLY PHE ILE GLN ASP ARG ALA GLY ARG MET ALA SEQRES 4 A 192 GLY GLU THR PRO GLU LEU THR LEU GLU GLN PRO PRO GLN SEQRES 5 A 192 ASP ALA SER THR LYS LYS LEU SER GLU SER LEU ARG ARG SEQRES 6 A 192 ILE GLY ASP GLU LEU ASP SER ASN MET GLU LEU GLN ARG SEQRES 7 A 192 MET ILE ALA ASP VAL ASP THR ASP SER PRO ARG GLU VAL SEQRES 8 A 192 PHE PHE ARG VAL ALA ALA ASP MET PHE ALA ASP GLY ASN SEQRES 9 A 192 PHE ASN TRP GLY ARG VAL VAL ALA LEU PHE TYR PHE ALA SEQRES 10 A 192 SER LYS LEU VAL LEU LYS ALA LEU SER THR LYS VAL PRO SEQRES 11 A 192 GLU LEU ILE ARG THR ILE MET GLY TRP THR LEU ASP PHE SEQRES 12 A 192 LEU ARG GLU ARG LEU LEU VAL TRP ILE GLN ASP GLN GLY SEQRES 13 A 192 GLY TRP GLU GLY LEU LEU SER TYR PHE GLY THR PRO THR SEQRES 14 A 192 TRP GLN THR VAL THR ILE PHE VAL ALA GLY VAL LEU THR SEQRES 15 A 192 ALA SER LEU THR ILE TRP LYS LYS MET GLY HET SO4 A 201 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *26(H2 O) HELIX 1 AA1 SER A 15 ALA A 35 1 21 HELIX 2 AA2 ALA A 54 ASP A 71 1 18 HELIX 3 AA3 ASN A 73 ASP A 82 1 10 HELIX 4 AA4 SER A 87 PHE A 100 1 14 HELIX 5 AA5 ASN A 106 LEU A 125 1 20 HELIX 6 AA6 GLU A 131 LEU A 148 1 18 HELIX 7 AA7 LEU A 148 GLN A 155 1 8 HELIX 8 AA8 TRP A 158 GLY A 166 1 9 HELIX 9 AA9 THR A 169 GLN A 171 5 3 HELIX 10 AB1 THR A 172 LYS A 189 1 18 SITE 1 AC1 5 SER A 16 TRP A 139 PRO A 168 THR A 169 SITE 2 AC1 5 HOH A 305 CRYST1 40.787 51.950 62.985 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 0.024518 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019249 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015877 0.00000