PDB Short entry for 4QVF HEADER APOPTOSIS 15-JUL-14 4QVF TITLE CRYSTAL STRUCTURE OF BCL-XL IN COMPLEX WITH BIM BH3 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: BCL-2-LIKE PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-209; COMPND 5 SYNONYM: BCL2-L-1, APOPTOSIS REGULATOR BCL-X; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: PEPTIDE FROM BCL-2-LIKE PROTEIN 11; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: UNP RESIDUES 141-166; COMPND 11 SYNONYM: BCL2-L-11, BCL2-INTERACTING MEDIATOR OF CELL DEATH; COMPND 12 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: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PETSUMO; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606; SOURCE 16 OTHER_DETAILS: THIS BIM BH3 SEQUENCE OCCURS NATURALLY IN HUMANS KEYWDS PROTEIN-PEPTIDE COMPLEX, BCL-2 LIKE, HETERODIMER, APOPTOSIS, ANTI- KEYWDS 2 APOPTOTIC, BH3 BINDING, BIM BH3 EXPDTA X-RAY DIFFRACTION AUTHOR R.SREEKANTH,H.S.YOON REVDAT 3 08-NOV-23 4QVF 1 REMARK REVDAT 2 24-AUG-22 4QVF 1 JRNL SEQADV REVDAT 1 10-JUN-15 4QVF 0 JRNL AUTH S.RAJAN,M.CHOI,K.BAEK,H.S.YOON JRNL TITL BH3 INDUCED CONFORMATIONAL CHANGES IN BCL-XL REVEALED BY JRNL TITL 2 CRYSTAL STRUCTURE AND COMPARATIVE ANALYSIS. JRNL REF PROTEINS V. 83 1262 2015 JRNL REFN ESSN 1097-0134 JRNL PMID 25907960 JRNL DOI 10.1002/PROT.24816 REMARK 2 REMARK 2 RESOLUTION. 1.53 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) 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) : 1.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.3 REMARK 3 NUMBER OF REFLECTIONS : 22740 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.040 REMARK 3 FREE R VALUE TEST SET COUNT : 918 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 31.8543 - 2.9282 0.97 3427 158 0.1693 0.2223 REMARK 3 2 2.9282 - 2.3244 0.98 3468 105 0.1655 0.2282 REMARK 3 3 2.3244 - 2.0307 0.97 3388 138 0.1574 0.2260 REMARK 3 4 2.0307 - 1.8450 0.96 3360 151 0.1683 0.2500 REMARK 3 5 1.8450 - 1.7128 0.97 3339 161 0.1622 0.2516 REMARK 3 6 1.7128 - 1.6118 0.91 3167 133 0.1534 0.2325 REMARK 3 7 1.6118 - 1.5311 0.48 1673 72 0.1440 0.2015 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.700 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.12 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 1364 REMARK 3 ANGLE : 0.878 1847 REMARK 3 CHIRALITY : 0.037 191 REMARK 3 PLANARITY : 0.004 238 REMARK 3 DIHEDRAL : 13.238 481 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 4QVF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-AUG-14. REMARK 100 THE DEPOSITION ID IS D_1000086562. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUL-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL13B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24769 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.530 REMARK 200 RESOLUTION RANGE LOW (A) : 31.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.53 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.58000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.500 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: 4EHR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 17.5% PEG 8000, 0.2M NACL, 0.1M REMARK 280 PHOSPHATE CITRATE PH 4.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 53.77000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.97500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 53.77000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.97500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 415 LIES ON A SPECIAL POSITION. 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 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 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 ASP B 51 REMARK 465 MET B 52 REMARK 465 ARG B 53 REMARK 465 ARG B 75 REMARK 465 ARG B 76 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MAZ RELATED DB: PDB REMARK 900 RELATED ID: 4QVE RELATED DB: PDB DBREF 4QVF A 1 209 UNP Q07817 B2CL1_HUMAN 1 209 DBREF 4QVF B 51 76 UNP O43521 B2L11_HUMAN 141 166 SEQADV 4QVF A UNP Q07817 MET 45 DELETION SEQADV 4QVF A UNP Q07817 GLU 46 DELETION SEQADV 4QVF A UNP Q07817 THR 47 DELETION SEQADV 4QVF A UNP Q07817 PRO 48 DELETION SEQADV 4QVF A UNP Q07817 SER 49 DELETION SEQADV 4QVF A UNP Q07817 ALA 50 DELETION SEQADV 4QVF A UNP Q07817 ILE 51 DELETION SEQADV 4QVF A UNP Q07817 ASN 52 DELETION SEQADV 4QVF A UNP Q07817 GLY 53 DELETION SEQADV 4QVF A UNP Q07817 ASN 54 DELETION SEQADV 4QVF A UNP Q07817 PRO 55 DELETION SEQADV 4QVF A UNP Q07817 SER 56 DELETION SEQADV 4QVF A UNP Q07817 TRP 57 DELETION SEQADV 4QVF A UNP Q07817 HIS 58 DELETION SEQADV 4QVF A UNP Q07817 LEU 59 DELETION SEQADV 4QVF A UNP Q07817 ALA 60 DELETION SEQADV 4QVF A UNP Q07817 ASP 61 DELETION SEQADV 4QVF A UNP Q07817 SER 62 DELETION SEQADV 4QVF A UNP Q07817 PRO 63 DELETION SEQADV 4QVF A UNP Q07817 ALA 64 DELETION SEQADV 4QVF A UNP Q07817 VAL 65 DELETION SEQADV 4QVF A UNP Q07817 ASN 66 DELETION SEQADV 4QVF A UNP Q07817 GLY 67 DELETION SEQADV 4QVF A UNP Q07817 ALA 68 DELETION SEQADV 4QVF A UNP Q07817 THR 69 DELETION SEQADV 4QVF A UNP Q07817 GLY 70 DELETION SEQADV 4QVF A UNP Q07817 HIS 71 DELETION SEQADV 4QVF A UNP Q07817 SER 72 DELETION SEQADV 4QVF A UNP Q07817 SER 73 DELETION SEQADV 4QVF A UNP Q07817 SER 74 DELETION SEQADV 4QVF A UNP Q07817 LEU 75 DELETION SEQADV 4QVF A UNP Q07817 ASP 76 DELETION SEQADV 4QVF A UNP Q07817 ALA 77 DELETION SEQADV 4QVF A UNP Q07817 ARG 78 DELETION SEQADV 4QVF A UNP Q07817 GLU 79 DELETION SEQADV 4QVF A UNP Q07817 VAL 80 DELETION SEQADV 4QVF A UNP Q07817 ILE 81 DELETION SEQADV 4QVF A UNP Q07817 PRO 82 DELETION SEQADV 4QVF A UNP Q07817 MET 83 DELETION SEQADV 4QVF A UNP Q07817 ALA 84 DELETION SEQRES 1 A 169 MET SER GLN SER ASN ARG GLU LEU VAL VAL ASP PHE LEU SEQRES 2 A 169 SER TYR LYS LEU SER GLN LYS GLY TYR SER TRP SER GLN SEQRES 3 A 169 PHE SER ASP VAL GLU GLU ASN ARG THR GLU ALA PRO GLU SEQRES 4 A 169 GLY THR GLU SER GLU ALA VAL LYS GLN ALA LEU ARG GLU SEQRES 5 A 169 ALA GLY ASP GLU PHE GLU LEU ARG TYR ARG ARG ALA PHE SEQRES 6 A 169 SER ASP LEU THR SER GLN LEU HIS ILE THR PRO GLY THR SEQRES 7 A 169 ALA TYR GLN SER PHE GLU GLN VAL VAL ASN GLU LEU PHE SEQRES 8 A 169 ARG ASP GLY VAL ASN TRP GLY ARG ILE VAL ALA PHE PHE SEQRES 9 A 169 SER PHE GLY GLY ALA LEU CYS VAL GLU SER VAL ASP LYS SEQRES 10 A 169 GLU MET GLN VAL LEU VAL SER ARG ILE ALA ALA TRP MET SEQRES 11 A 169 ALA THR TYR LEU ASN ASP HIS LEU GLU PRO TRP ILE GLN SEQRES 12 A 169 GLU ASN GLY GLY TRP ASP THR PHE VAL GLU LEU TYR GLY SEQRES 13 A 169 ASN ASN ALA ALA ALA GLU SER ARG LYS GLY GLN GLU ARG SEQRES 1 B 26 ASP MET ARG PRO GLU ILE TRP ILE ALA GLN GLU LEU ARG SEQRES 2 B 26 ARG ILE GLY ASP GLU PHE ASN ALA TYR TYR ALA ARG ARG FORMUL 3 HOH *173(H2 O) HELIX 1 1 SER A 4 GLN A 19 1 16 HELIX 2 2 SER A 23 PHE A 27 5 5 HELIX 3 3 VAL A 86 PHE A 105 1 20 HELIX 4 4 ASP A 107 LEU A 112 1 6 HELIX 5 5 THR A 118 PHE A 131 1 14 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 187 GLY A 196 1 10 HELIX 10 10 GLU B 55 ALA B 74 1 20 CRYST1 107.540 47.950 34.180 90.00 105.03 90.00 C 1 2 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 0.009299 0.000000 0.002497 0.00000 SCALE2 0.000000 0.020855 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030293 0.00000