HEADER APOPTOSIS 09-APR-96 1MAZ TITLE X-RAY STRUCTURE OF BCL-XL, AN INHIBITOR OF PROGRAMMED CELL DEATH COMPND MOL_ID: 1; COMPND 2 MOLECULE: BCL-2-LIKE PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-209; COMPND 5 SYNONYM: APOPTOSIS REGULATOR BCL-X; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: BCL2L1, BCL2L, BCLX; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET29B KEYWDS APOPTOSIS, PROGRAMMED CELL DEATH, BCL-2 FAMILY EXPDTA X-RAY DIFFRACTION AUTHOR S.W.MUCHMORE,M.SATTLER,H.LIANG,R.P.MEADOWS,J.E.HARLAN,H.S.YOON, AUTHOR 2 D.NETTESHEIM,B.S.CHANG,C.B.THOMPSON,S.L.WONG,S.C.NG,S.W.FESIK REVDAT 5 14-FEB-24 1MAZ 1 REMARK REVDAT 4 02-JUN-10 1MAZ 1 COMPND REMARK SOURCE REVDAT 3 24-FEB-09 1MAZ 1 VERSN REVDAT 2 01-APR-03 1MAZ 1 JRNL REVDAT 1 21-APR-97 1MAZ 0 JRNL AUTH S.W.MUCHMORE,M.SATTLER,H.LIANG,R.P.MEADOWS,J.E.HARLAN, JRNL AUTH 2 H.S.YOON,D.NETTESHEIM,B.S.CHANG,C.B.THOMPSON,S.L.WONG, JRNL AUTH 3 S.L.NG,S.W.FESIK JRNL TITL X-RAY AND NMR STRUCTURE OF HUMAN BCL-XL, AN INHIBITOR OF JRNL TITL 2 PROGRAMMED CELL DEATH. JRNL REF NATURE V. 381 335 1996 JRNL REFN ISSN 0028-0836 JRNL PMID 8692274 JRNL DOI 10.1038/381335A0 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 11139 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1161 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 148 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1MAZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000174913. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-NOV-94 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11139 REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.05500 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) : NULL 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) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 55.25000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 31.75000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 31.75000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 27.62500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 31.75000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 31.75000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 82.87500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 31.75000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 31.75000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 27.62500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 31.75000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 31.75000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 82.87500 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 55.25000 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 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 -3 REMARK 465 SER A -2 REMARK 465 MET A -1 REMARK 465 ALA A 0 REMARK 465 SER A 28 REMARK 465 ASP A 29 REMARK 465 VAL A 30 REMARK 465 GLU A 31 REMARK 465 GLU A 32 REMARK 465 ASN A 33 REMARK 465 ARG A 34 REMARK 465 THR A 35 REMARK 465 GLU A 36 REMARK 465 ALA A 37 REMARK 465 PRO A 38 REMARK 465 GLU A 39 REMARK 465 GLY A 40 REMARK 465 THR A 41 REMARK 465 GLU A 42 REMARK 465 SER A 43 REMARK 465 GLU A 44 REMARK 465 MET A 45 REMARK 465 GLU A 46 REMARK 465 THR A 47 REMARK 465 PRO A 48 REMARK 465 SER A 49 REMARK 465 ALA A 50 REMARK 465 ILE A 51 REMARK 465 ASN A 52 REMARK 465 GLY A 53 REMARK 465 ASN A 54 REMARK 465 PRO A 55 REMARK 465 SER A 56 REMARK 465 TRP A 57 REMARK 465 HIS A 58 REMARK 465 LEU A 59 REMARK 465 ALA A 60 REMARK 465 ASP A 61 REMARK 465 SER A 62 REMARK 465 PRO A 63 REMARK 465 ALA A 64 REMARK 465 VAL A 65 REMARK 465 ASN A 66 REMARK 465 GLY A 67 REMARK 465 ALA A 68 REMARK 465 THR A 69 REMARK 465 GLY A 70 REMARK 465 HIS A 71 REMARK 465 SER A 72 REMARK 465 SER A 73 REMARK 465 SER A 74 REMARK 465 LEU A 75 REMARK 465 ASP A 76 REMARK 465 ALA A 77 REMARK 465 ARG A 78 REMARK 465 GLU A 79 REMARK 465 VAL A 80 REMARK 465 ASN A 197 REMARK 465 ASN A 198 REMARK 465 ALA A 199 REMARK 465 ALA A 200 REMARK 465 ALA A 201 REMARK 465 GLU A 202 REMARK 465 SER A 203 REMARK 465 ARG A 204 REMARK 465 LYS A 205 REMARK 465 GLY A 206 REMARK 465 GLN A 207 REMARK 465 GLU A 208 REMARK 465 ARG A 209 REMARK 465 LEU A 210 REMARK 465 GLU A 211 REMARK 465 HIS A 212 REMARK 465 HIS A 213 REMARK 465 HIS A 214 REMARK 465 HIS A 215 REMARK 465 HIS A 216 REMARK 465 HIS A 217 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 PRO A 82 42.66 -91.66 REMARK 500 HIS A 113 72.58 49.45 REMARK 500 TYR A 195 -147.85 -105.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BXL RELATED DB: PDB DBREF 1MAZ A 1 209 UNP Q07817 BCLX_HUMAN 1 209 SEQRES 1 A 221 MET SER MET ALA MET SER GLN SER ASN ARG GLU LEU VAL SEQRES 2 A 221 VAL ASP PHE LEU SER TYR LYS LEU SER GLN LYS GLY TYR SEQRES 3 A 221 SER TRP SER GLN PHE SER ASP VAL GLU GLU ASN ARG THR SEQRES 4 A 221 GLU ALA PRO GLU GLY THR GLU SER GLU MET GLU THR PRO SEQRES 5 A 221 SER ALA ILE ASN GLY ASN PRO SER TRP HIS LEU ALA ASP SEQRES 6 A 221 SER PRO ALA VAL ASN GLY ALA THR GLY HIS SER SER SER SEQRES 7 A 221 LEU ASP ALA ARG GLU VAL ILE PRO MET ALA ALA VAL LYS SEQRES 8 A 221 GLN ALA LEU ARG GLU ALA GLY ASP GLU PHE GLU LEU ARG SEQRES 9 A 221 TYR ARG ARG ALA PHE SER ASP LEU THR SER GLN LEU HIS SEQRES 10 A 221 ILE THR PRO GLY THR ALA TYR GLN SER PHE GLU GLN VAL SEQRES 11 A 221 VAL ASN GLU LEU PHE ARG ASP GLY VAL ASN TRP GLY ARG SEQRES 12 A 221 ILE VAL ALA PHE PHE SER PHE GLY GLY ALA LEU CYS VAL SEQRES 13 A 221 GLU SER VAL ASP LYS GLU MET GLN VAL LEU VAL SER ARG SEQRES 14 A 221 ILE ALA ALA TRP MET ALA THR TYR LEU ASN ASP HIS LEU SEQRES 15 A 221 GLU PRO TRP ILE GLN GLU ASN GLY GLY TRP ASP THR PHE SEQRES 16 A 221 VAL GLU LEU TYR GLY ASN ASN ALA ALA ALA GLU SER ARG SEQRES 17 A 221 LYS GLY GLN GLU ARG LEU GLU HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *148(H2 O) HELIX 1 1 SER A 2 GLN A 19 1 18 HELIX 2 2 ALA A 84 ARG A 100 1 17 HELIX 3 3 SER A 106 LEU A 112 1 7 HELIX 4 4 TYR A 120 PHE A 131 1 12 HELIX 5 5 TRP A 137 ASP A 156 1 20 HELIX 6 6 GLN A 160 HIS A 177 5 18 HELIX 7 7 GLU A 179 GLU A 184 1 6 HELIX 8 8 GLY A 187 LEU A 194 1 8 CRYST1 63.500 63.500 110.500 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 0.015748 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015748 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009050 0.00000