HEADER APOPTOSIS 17-JUN-15 5C3G TITLE CRYSTAL STRUCTURE OF BCL-XL BOUND TO BIM-MM COMPND MOL_ID: 1; COMPND 2 MOLECULE: BCL-2-LIKE PROTEIN 1,BCL-2-LIKE PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-26,UNP RESIDUES 83-209; COMPND 5 SYNONYM: BCL2-L-1,APOPTOSIS REGULATOR BCL-X, BCL-XL,BCL2-L-1, COMPND 6 APOPTOSIS REGULATOR BCL-X,BCL-XL; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: DELETION MUTATION PERFORMED TO REMOVE FLEXIBLE LOOP, COMPND 9 REMOVING RESIDUES 27-82. NUMBERING IS CORRECT IN THE PDB FILE.; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: BCL-2-LIKE PROTEIN 11; COMPND 12 CHAIN: B; COMPND 13 FRAGMENT: UNP RESIDUES 56-76; COMPND 14 SYNONYM: BCL2-L-11,BCL2-INTERACTING MEDIATOR OF CELL DEATH; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS, HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE, HUMAN; SOURCE 4 ORGANISM_TAXID: 10090, 9606; SOURCE 5 GENE: BCL2L1, BCL2L, BCLX, BCL2L1, BCL2L, BCLX; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS COMPLEX, BCL-2 FAMILY, BH3, STAPLED PEPTIDE, APOPTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR J.A.MILES,D.J.YEO,P.ROWELL,S.RODRIGUEZ-MARIN,C.M.PASK,S.L.WARRINER, AUTHOR 2 T.A.EDWARDS,A.J.WILSON REVDAT 3 10-JAN-24 5C3G 1 REMARK REVDAT 2 18-OCT-17 5C3G 1 JRNL REVDAT 1 20-APR-16 5C3G 0 JRNL AUTH J.A.MILES,D.J.YEO,P.ROWELL,S.RODRIGUEZ-MARIN,C.M.PASK, JRNL AUTH 2 S.L.WARRINER,T.A.EDWARDS,A.J.WILSON JRNL TITL HYDROCARBON CONSTRAINED PEPTIDES - UNDERSTANDING JRNL TITL 2 PREORGANISATION AND BINDING AFFINITY. JRNL REF CHEM SCI V. 7 3694 2016 JRNL REFN ISSN 2041-6520 JRNL PMID 28970875 JRNL DOI 10.1039/C5SC04048E REMARK 2 REMARK 2 RESOLUTION. 2.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 11577 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 581 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 34.7721 - 3.8883 0.98 2911 155 0.1962 0.2455 REMARK 3 2 3.8883 - 3.0869 0.98 2753 138 0.2453 0.2883 REMARK 3 3 3.0869 - 2.6969 0.97 2686 133 0.2778 0.3167 REMARK 3 4 2.6969 - 2.4504 0.97 2646 155 0.2973 0.3758 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) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.910 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 : 0.003 1297 REMARK 3 ANGLE : 0.691 1754 REMARK 3 CHIRALITY : 0.029 181 REMARK 3 PLANARITY : 0.002 228 REMARK 3 DIHEDRAL : 12.954 459 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 5C3G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-JUN-15. REMARK 100 THE DEPOSITION ID IS D_1000210963. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-JAN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 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 : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11587 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450 REMARK 200 RESOLUTION RANGE LOW (A) : 45.990 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 8.700 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.30 REMARK 200 R MERGE FOR SHELL (I) : 0.87200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.390 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: 3FDL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% PEG 1500, 0.1M SODIUM ACETATE PH REMARK 280 5.5, 2.5M NACL, 1.5% MPD, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z+1/2 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 46.38000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 46.38000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 46.38000 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 46.38000 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 46.38000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 46.38000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -52.0 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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 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 SER A 2 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 ACE B 87 REMARK 465 ILE B 88 REMARK 465 TRP B 89 REMARK 465 ALA B 106 REMARK 465 ARG B 107 REMARK 465 ARG B 108 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 PHE A 12 -58.15 74.06 REMARK 500 GLN A 26 40.24 -98.54 REMARK 500 PHE A 105 -126.28 -130.83 REMARK 500 VAL A 155 -53.66 72.14 REMARK 500 ASN A 185 38.12 -99.69 REMARK 500 TYR A 195 68.58 -115.95 REMARK 500 REMARK 500 REMARK: NULL DBREF 5C3G A 1 26 UNP Q64373 B2CL1_MOUSE 1 26 DBREF 5C3G A 83 209 UNP Q07817 B2CL1_HUMAN 83 209 DBREF 5C3G B 88 108 UNP O43521 B2L11_HUMAN 56 76 SEQADV 5C3G ACE B 87 UNP O43521 ACETYLATION SEQADV 5C3G NLE B 96 UNP O43521 ARG 64 ENGINEERED MUTATION SEQADV 5C3G NLE B 100 UNP O43521 GLU 68 ENGINEERED MUTATION SEQRES 1 A 153 MET SER GLN SER ASN ARG GLU LEU VAL VAL ASP PHE LEU SEQRES 2 A 153 SER TYR LYS LEU SER GLN LYS GLY TYR SER TRP SER GLN SEQRES 3 A 153 MET ALA ALA VAL LYS GLN ALA LEU ARG GLU ALA GLY ASP SEQRES 4 A 153 GLU PHE GLU LEU ARG TYR ARG ARG ALA PHE SER ASP LEU SEQRES 5 A 153 THR SER GLN LEU HIS ILE THR PRO GLY THR ALA TYR GLN SEQRES 6 A 153 SER PHE GLU GLN VAL VAL ASN GLU LEU PHE ARG ASP GLY SEQRES 7 A 153 VAL ASN TRP GLY ARG ILE VAL ALA PHE PHE SER PHE GLY SEQRES 8 A 153 GLY ALA LEU CYS VAL GLU SER VAL ASP LYS GLU MET GLN SEQRES 9 A 153 VAL LEU VAL SER ARG ILE ALA ALA TRP MET ALA THR TYR SEQRES 10 A 153 LEU ASN ASP HIS LEU GLU PRO TRP ILE GLN GLU ASN GLY SEQRES 11 A 153 GLY TRP ASP THR PHE VAL GLU LEU TYR GLY ASN ASN ALA SEQRES 12 A 153 ALA ALA GLU SER ARG LYS GLY GLN GLU ARG SEQRES 1 B 22 ACE ILE TRP ILE ALA GLN GLU LEU ARG NLE ILE GLY ASP SEQRES 2 B 22 NLE PHE ASN ALA TYR TYR ALA ARG ARG HET NLE B 96 16 HET NLE B 100 15 HETNAM NLE NORLEUCINE FORMUL 2 NLE 2(C6 H13 N O2) FORMUL 3 HOH *3(H2 O) HELIX 1 AA1 GLN A 3 GLN A 19 1 17 HELIX 2 AA2 MET A 83 PHE A 105 1 23 HELIX 3 AA3 THR A 118 PHE A 131 1 14 HELIX 4 AA4 ASN A 136 LYS A 157 1 22 HELIX 5 AA5 VAL A 161 HIS A 177 1 17 HELIX 6 AA6 LEU A 178 ASN A 185 1 8 HELIX 7 AA7 GLY A 186 TYR A 195 1 10 HELIX 8 AA8 ALA B 91 TYR B 105 1 15 LINK C ARG B 95 N NLE B 96 1555 1555 1.33 LINK C NLE B 96 N ILE B 97 1555 1555 1.33 LINK CE NLE B 96 CE NLE B 100 1555 1555 1.49 LINK C ASP B 99 N NLE B 100 1555 1555 1.33 LINK C NLE B 100 N PHE B 101 1555 1555 1.33 CRYST1 106.220 106.220 92.760 90.00 90.00 120.00 P 63 2 2 12 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 0.009414 0.005435 0.000000 0.00000 SCALE2 0.000000 0.010871 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010781 0.00000