HEADER APOPTOSIS 17-JUN-03 1PQ0 TITLE CRYSTAL STRUCTURE OF MOUSE BCL-XL COMPND MOL_ID: 1; COMPND 2 MOLECULE: APOPTOSIS REGULATOR BCL-X; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: BCL-XL; COMPND 5 SYNONYM: BCL2-LIKE 1 PROTEIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: BCL2L1 OR BCL2L OR BCLX; SOURCE 6 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 7 EXPRESSION_SYSTEM_COMMON: CABBAGE LOOPER; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: HI FIVE; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 11 EXPRESSION_SYSTEM_VECTOR: BACVECTOR 3000 (NOVAGEN) KEYWDS BCL-XL, APOPTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR X.LIU,S.DAI,Y.ZHU,P.MARRACK,J.W.KAPPLER REVDAT 3 16-AUG-23 1PQ0 1 REMARK REVDAT 2 24-FEB-09 1PQ0 1 VERSN REVDAT 1 23-SEP-03 1PQ0 0 JRNL AUTH X.LIU,S.DAI,Y.ZHU,P.MARRACK,J.W.KAPPLER JRNL TITL THE STRUCTURE OF A BCL-XL/BIM FRAGMENT COMPLEX: IMPLICATIONS JRNL TITL 2 FOR BIM FUNCTION JRNL REF IMMUNITY V. 19 341 2003 JRNL REFN ISSN 1074-7613 JRNL PMID 14499110 JRNL DOI 10.1016/S1074-7613(03)00234-6 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.79 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) (%) : 93.7 REMARK 3 NUMBER OF REFLECTIONS : 11227 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 525 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.011 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1563 REMARK 3 BIN R VALUE (WORKING SET) : 0.2430 REMARK 3 BIN FREE R VALUE : 0.2700 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 74 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.031 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1165 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 108 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.51000 REMARK 3 B22 (A**2) : 2.51000 REMARK 3 B33 (A**2) : -5.02000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM SIGMAA (A) : 0.20 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.29 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.20 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 18.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.680 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 47.10 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : &_1_PARAMETER_INFILE_3 REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1PQ0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-JUN-03. REMARK 100 THE DEPOSITION ID IS D_1000019485. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-NOV-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : DOUBLE-CRYSTAL, SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11386 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.08700 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) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.08700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 9.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1AF3, RAT BCL-XL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NH4SO4, MES, PH 6.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K 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 54.80000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 31.80500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 31.80500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 27.40000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 31.80500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 31.80500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 82.20000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 31.80500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 31.80500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 27.40000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 31.80500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 31.80500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 82.20000 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 54.80000 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 1 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 GLU A 40 REMARK 465 THR A 41 REMARK 465 GLU A 42 REMARK 465 ALA A 43 REMARK 465 GLU A 44 REMARK 465 ARG 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 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 29 CG OD1 OD2 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 GLN A 26 1.46 -64.58 REMARK 500 PHE A 27 -68.82 -92.65 REMARK 500 SER A 28 -85.81 -64.46 REMARK 500 PRO A 82 -174.53 -56.01 REMARK 500 ARG A 103 5.02 -68.12 REMARK 500 ALA A 104 44.21 33.03 REMARK 500 HIS A 113 66.24 32.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1PQ1 RELATED DB: PDB REMARK 900 COMPLEX WITH BIM DBREF 1PQ0 A 1 196 UNP Q64373 BCLX_MOUSE 1 196 SEQRES 1 A 196 MET SER GLN SER ASN ARG GLU LEU VAL VAL ASP PHE LEU SEQRES 2 A 196 SER TYR LYS LEU SER GLN LYS GLY TYR SER TRP SER GLN SEQRES 3 A 196 PHE SER ASP VAL GLU GLU ASN ARG THR GLU ALA PRO GLU SEQRES 4 A 196 GLU THR GLU ALA GLU ARG GLU THR PRO SER ALA ILE ASN SEQRES 5 A 196 GLY ASN PRO SER TRP HIS LEU ALA ASP SER PRO ALA VAL SEQRES 6 A 196 ASN GLY ALA THR GLY HIS SER SER SER LEU ASP ALA ARG SEQRES 7 A 196 GLU VAL ILE PRO MET ALA ALA VAL LYS GLN ALA LEU ARG SEQRES 8 A 196 GLU ALA GLY ASP GLU PHE GLU LEU ARG TYR ARG ARG ALA SEQRES 9 A 196 PHE SER ASP LEU THR SER GLN LEU HIS ILE THR PRO GLY SEQRES 10 A 196 THR ALA TYR GLN SER PHE GLU GLN VAL VAL ASN GLU LEU SEQRES 11 A 196 PHE ARG ASP GLY VAL ASN TRP GLY ARG ILE VAL ALA PHE SEQRES 12 A 196 PHE SER PHE GLY GLY ALA LEU CYS VAL GLU SER VAL ASP SEQRES 13 A 196 LYS GLU MET GLN VAL LEU VAL SER ARG ILE ALA SER TRP SEQRES 14 A 196 MET ALA THR TYR LEU ASN ASP HIS LEU GLU PRO TRP ILE SEQRES 15 A 196 GLN GLU ASN GLY GLY TRP ASP THR PHE VAL ASP LEU TYR SEQRES 16 A 196 GLY FORMUL 2 HOH *108(H2 O) HELIX 1 1 SER A 2 LYS A 20 1 19 HELIX 2 2 MET A 83 TYR A 101 1 19 HELIX 3 3 PHE A 105 HIS A 113 1 9 HELIX 4 4 ALA A 119 GLU A 129 1 11 HELIX 5 5 LEU A 130 ARG A 132 5 3 HELIX 6 6 ASN A 136 LYS A 157 1 22 HELIX 7 7 VAL A 161 LEU A 178 1 18 HELIX 8 8 LEU A 178 ASN A 185 1 8 HELIX 9 9 GLY A 186 GLY A 196 1 11 CRYST1 63.610 63.610 109.600 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 0.015721 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015721 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009124 0.00000