HEADER APOPTOSIS 04-JAN-15 4S0P TITLE CRYSTAL STRUCTURE OF THE AUTOINHIBITED DIMER OF PRO-APOPTOTIC BAX (II) COMPND MOL_ID: 1; COMPND 2 MOLECULE: APOPTOSIS REGULATOR BAX; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: BCL-2-LIKE PROTEIN 4, BCL2-L-4; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES 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 BCL-2 FAMILY PROTEIN, APOPTOSIS REGULATOR, AUTOINHIBITED DIMER, KEYWDS 2 APOPTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR A.PRIYADARSHI,E.GAVATHIOTIS REVDAT 5 20-SEP-23 4S0P 1 SEQADV REVDAT 4 17-JUL-19 4S0P 1 REMARK REVDAT 3 22-NOV-17 4S0P 1 REMARK REVDAT 2 17-AUG-16 4S0P 1 JRNL REMARK REVDAT 1 20-JUL-16 4S0P 0 JRNL AUTH T.P.GARNER,D.E.REYNA,A.PRIYADARSHI,H.C.CHEN,S.LI,Y.WU, JRNL AUTH 2 Y.T.GANESAN,V.N.MALASHKEVICH,S.S.ALMO,E.H.CHENG, JRNL AUTH 3 E.GAVATHIOTIS JRNL TITL AN AUTOINHIBITED DIMERIC FORM OF BAX REGULATES THE BAX JRNL TITL 2 ACTIVATION PATHWAY. JRNL REF MOL.CELL V. 63 485 2016 JRNL REFN ISSN 1097-2765 JRNL PMID 27425408 JRNL DOI 10.1016/J.MOLCEL.2016.06.010 REMARK 2 REMARK 2 RESOLUTION. 3.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_1839 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.550 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.9 REMARK 3 NUMBER OF REFLECTIONS : 4859 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.270 REMARK 3 FREE R VALUE TEST SET COUNT : 256 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 46.1773 - 4.0963 0.94 2415 166 0.2135 0.2672 REMARK 3 2 4.0963 - 3.2516 0.84 2188 90 0.2056 0.2748 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) : 0.380 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.340 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 : 0.011 2812 REMARK 3 ANGLE : 1.265 3806 REMARK 3 CHIRALITY : 0.052 434 REMARK 3 PLANARITY : 0.007 476 REMARK 3 DIHEDRAL : 19.512 1022 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 4S0P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JAN-15. REMARK 100 THE DEPOSITION ID IS D_1000088032. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4866 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.250 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.3 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: MOLECULAR REPLACEMENT REMARK 200 STARTING MODEL: 1F16 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6 M AMMONIUM SULFATE, 0.1 M BIS REMARK 280 -TRIS, PH 6.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 32.50500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 1340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17120 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.14882 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 -32.50500 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 65.58983 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 40.58700 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 -32.50500 REMARK 350 BIOMT3 2 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 GLY A 11 REMARK 465 GLY A 12 REMARK 465 PRO A 13 REMARK 465 GLY A 36 REMARK 465 ARG A 37 REMARK 465 MET A 38 REMARK 465 GLY A 39 REMARK 465 GLY A 40 REMARK 465 MET B 1 REMARK 465 ASP B 2 REMARK 465 GLY B 3 REMARK 465 SER B 4 REMARK 465 GLY B 5 REMARK 465 GLU B 6 REMARK 465 GLN B 7 REMARK 465 PRO B 8 REMARK 465 ARG B 9 REMARK 465 GLY B 10 REMARK 465 GLY B 11 REMARK 465 GLY B 12 REMARK 465 PRO B 13 REMARK 465 GLY B 36 REMARK 465 ARG B 37 REMARK 465 MET B 38 REMARK 465 GLY B 39 REMARK 465 GLY B 40 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 LYS A 21 -70.77 -54.02 REMARK 500 ILE A 31 -81.69 -80.94 REMARK 500 PRO A 51 102.52 -55.64 REMARK 500 ASP A 53 -160.13 -127.72 REMARK 500 ASP A 84 108.11 -56.19 REMARK 500 ASP A 86 17.09 -144.53 REMARK 500 TRP A 170 -78.23 -46.72 REMARK 500 LYS B 21 -75.44 -53.39 REMARK 500 ASP B 33 -74.81 -60.04 REMARK 500 PRO B 51 96.07 -58.72 REMARK 500 GLN B 52 100.59 -44.68 REMARK 500 ASP B 86 16.28 -145.33 REMARK 500 THR B 169 61.26 -108.35 REMARK 500 TRP B 170 -89.62 -77.37 REMARK 500 GLN B 171 4.37 -52.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4S0O RELATED DB: PDB REMARK 900 RELATED ID: 1F16 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF A PRO-APOPTOTIC PROTEIN BAX DBREF 4S0P A 1 192 UNP Q07812 BAX_HUMAN 1 192 DBREF 4S0P B 1 192 UNP Q07812 BAX_HUMAN 1 192 SEQADV 4S0P ARG A 67 UNP Q07812 GLY 67 ENGINEERED MUTATION SEQADV 4S0P ARG B 67 UNP Q07812 GLY 67 ENGINEERED MUTATION SEQRES 1 A 192 MET ASP GLY SER GLY GLU GLN PRO ARG GLY GLY GLY PRO SEQRES 2 A 192 THR SER SER GLU GLN ILE MET LYS THR GLY ALA LEU LEU SEQRES 3 A 192 LEU GLN GLY PHE ILE GLN ASP ARG ALA GLY ARG MET GLY SEQRES 4 A 192 GLY GLU ALA PRO GLU LEU ALA LEU ASP PRO VAL PRO GLN SEQRES 5 A 192 ASP ALA SER THR LYS LYS LEU SER GLU CYS LEU LYS ARG SEQRES 6 A 192 ILE ARG ASP GLU LEU ASP SER ASN MET GLU LEU GLN ARG SEQRES 7 A 192 MET ILE ALA ALA VAL ASP THR ASP SER PRO ARG GLU VAL SEQRES 8 A 192 PHE PHE ARG VAL ALA ALA ASP MET PHE SER 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 CYS 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 GLY TRP ILE GLN ASP GLN GLY SEQRES 13 A 192 GLY TRP ASP 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 SEQRES 1 B 192 MET ASP GLY SER GLY GLU GLN PRO ARG GLY GLY GLY PRO SEQRES 2 B 192 THR SER SER GLU GLN ILE MET LYS THR GLY ALA LEU LEU SEQRES 3 B 192 LEU GLN GLY PHE ILE GLN ASP ARG ALA GLY ARG MET GLY SEQRES 4 B 192 GLY GLU ALA PRO GLU LEU ALA LEU ASP PRO VAL PRO GLN SEQRES 5 B 192 ASP ALA SER THR LYS LYS LEU SER GLU CYS LEU LYS ARG SEQRES 6 B 192 ILE ARG ASP GLU LEU ASP SER ASN MET GLU LEU GLN ARG SEQRES 7 B 192 MET ILE ALA ALA VAL ASP THR ASP SER PRO ARG GLU VAL SEQRES 8 B 192 PHE PHE ARG VAL ALA ALA ASP MET PHE SER ASP GLY ASN SEQRES 9 B 192 PHE ASN TRP GLY ARG VAL VAL ALA LEU PHE TYR PHE ALA SEQRES 10 B 192 SER LYS LEU VAL LEU LYS ALA LEU CYS THR LYS VAL PRO SEQRES 11 B 192 GLU LEU ILE ARG THR ILE MET GLY TRP THR LEU ASP PHE SEQRES 12 B 192 LEU ARG GLU ARG LEU LEU GLY TRP ILE GLN ASP GLN GLY SEQRES 13 B 192 GLY TRP ASP GLY LEU LEU SER TYR PHE GLY THR PRO THR SEQRES 14 B 192 TRP GLN THR VAL THR ILE PHE VAL ALA GLY VAL LEU THR SEQRES 15 B 192 ALA SER LEU THR ILE TRP LYS LYS MET GLY HELIX 1 1 SER A 15 ASP A 33 1 19 HELIX 2 2 ALA A 54 SER A 72 1 19 HELIX 3 3 ASN A 73 ALA A 82 1 10 HELIX 4 4 PRO A 88 PHE A 100 1 13 HELIX 5 5 ASN A 106 CYS A 126 1 21 HELIX 6 6 GLU A 131 ASP A 154 1 24 HELIX 7 7 GLN A 155 GLY A 156 5 2 HELIX 8 8 GLY A 157 TRP A 158 5 2 HELIX 9 9 ASP A 159 TYR A 164 1 6 HELIX 10 10 THR A 169 GLY A 192 1 24 HELIX 11 11 SER B 15 ARG B 34 1 20 HELIX 12 12 ASP B 53 SER B 72 1 20 HELIX 13 13 ASN B 73 ALA B 82 1 10 HELIX 14 14 SER B 87 PHE B 100 1 14 HELIX 15 15 ASN B 106 CYS B 126 1 21 HELIX 16 16 GLU B 131 ASP B 154 1 24 HELIX 17 17 GLN B 155 GLY B 157 5 3 HELIX 18 18 TRP B 158 TYR B 164 1 7 HELIX 19 19 THR B 169 GLY B 192 1 24 CRYST1 40.587 65.010 65.590 90.00 89.87 90.00 P 1 21 1 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 0.024638 0.000000 -0.000056 0.00000 SCALE2 0.000000 0.015382 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015246 0.00000