HEADER REGULATORY PROTEIN 21-MAR-97 1AF3 TITLE RAT BCL-XL AN APOPTOSIS INHIBITORY PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: APOPTOSIS REGULATOR BCL-X; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SOLUBLE REGION; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BCL-XL, APOPTOSIS, MITOCHONDRION, ALTERNATIVE SPLICING, REGULATORY KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.ARITOMI,N.KUNISHIMA,N.INOHARA,Y.ISHIBASHI,S.OHTA,K.MORIKAWA REVDAT 4 07-FEB-24 1AF3 1 REMARK REVDAT 3 04-APR-18 1AF3 1 REMARK REVDAT 2 24-FEB-09 1AF3 1 VERSN REVDAT 1 07-JUL-97 1AF3 0 JRNL AUTH M.ARITOMI,N.KUNISHIMA,N.INOHARA,Y.ISHIBASHI,S.OHTA, JRNL AUTH 2 K.MORIKAWA JRNL TITL CRYSTAL STRUCTURE OF RAT BCL-XL. IMPLICATIONS FOR THE JRNL TITL 2 FUNCTION OF THE BCL-2 PROTEIN FAMILY. JRNL REF J.BIOL.CHEM. V. 272 27886 1997 JRNL REFN ISSN 0021-9258 JRNL PMID 9346936 JRNL DOI 10.1074/JBC.272.44.27886 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 8564 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 + TEST SET) : 0.225 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.500 REMARK 3 FREE R VALUE TEST SET COUNT : 560 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1175 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 51 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; 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 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1AF3 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_1000170737. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : SEP-96 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : MACSCIENCE M18X REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MACSCIENCE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8614 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : 0.10900 REMARK 200 R SYM (I) : 0.10900 REMARK 200 FOR THE DATA SET : 6.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : 0.96200 REMARK 200 R SYM FOR SHELL (I) : 0.96200 REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 5.6 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 56.13500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 32.02500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 32.02500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.06750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 32.02500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 32.02500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 84.20250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 32.02500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 32.02500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 28.06750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 32.02500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 32.02500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 84.20250 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 56.13500 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 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 PRO 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 91 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 GLU A 98 OE1 - CD - OE2 ANGL. DEV. = 8.1 DEGREES REMARK 500 ARG A 100 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ASP A 133 CB - CG - OD2 ANGL. DEV. = 9.3 DEGREES REMARK 500 ASN A 136 CB - CA - C ANGL. DEV. = -15.4 DEGREES REMARK 500 ARG A 165 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ASP A 193 OD1 - CG - OD2 ANGL. DEV. = 11.5 DEGREES REMARK 500 ASP A 193 CB - CG - OD2 ANGL. DEV. = -8.4 DEGREES 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 ASP A 29 68.05 -107.18 REMARK 500 ARG A 102 -79.73 -73.60 REMARK 500 REMARK 500 REMARK: NULL DBREF 1AF3 A 1 196 UNP P53563 BCLX_RAT 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 PRO 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 *51(H2 O) HELIX 1 1 GLN A 3 LYS A 20 1 18 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 ASN A 128 1 10 HELIX 5 5 GLU A 129 ARG A 132 5 4 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 64.050 64.050 112.270 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 0.015613 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015613 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008907 0.00000