HEADER APOPTOSIS 23-MAR-21 7M5A TITLE CRYSTAL STRUCTURE OF HUMAN BAK IN COMPLEX WITH W3W5_BID COMPND MOL_ID: 1; COMPND 2 MOLECULE: BCL-2 HOMOLOGOUS ANTAGONIST/KILLER; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: APOPTOSIS REGULATOR BAK,BCL-2-LIKE PROTEIN 7,BCL2-L-7; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: BH3-INTERACTING DOMAIN DEATH AGONIST P15; COMPND 8 CHAIN: B; COMPND 9 SYNONYM: P15 BID; COMPND 10 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: BAK1, BAK, BCL2L7, CDN1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: T7 PLACI/Y; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PNIC28BSA4; 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 KEYWDS PROTEIN-PEPTIDE COMPLEX, APOPTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR G.SINGH,A.AGGARWAL,T.MOLDOVEANU REVDAT 3 18-OCT-23 7M5A 1 REMARK REVDAT 2 03-AUG-22 7M5A 1 JRNL REVDAT 1 12-JAN-22 7M5A 0 JRNL AUTH G.SINGH,C.D.GUIBAO,J.SEETHARAMAN,A.AGGARWAL,C.R.GRACE, JRNL AUTH 2 D.E.MCNAMARA,S.VAITHIYALINGAM,M.B.WADDELL,T.MOLDOVEANU JRNL TITL STRUCTURAL BASIS OF BAK ACTIVATION IN MITOCHONDRIAL JRNL TITL 2 APOPTOSIS INITIATION. JRNL REF NAT COMMUN V. 13 250 2022 JRNL REFN ESSN 2041-1723 JRNL PMID 35017502 JRNL DOI 10.1038/S41467-021-27851-Y REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 26917 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.670 REMARK 3 FREE R VALUE TEST SET COUNT : 1257 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 35.6970 - 3.1191 0.99 3002 145 0.1774 0.2223 REMARK 3 2 3.1191 - 2.4759 0.99 2905 129 0.1913 0.1878 REMARK 3 3 2.4759 - 2.1630 0.99 2862 129 0.1702 0.2024 REMARK 3 4 2.1630 - 1.9652 1.00 2865 138 0.1762 0.1996 REMARK 3 5 1.9652 - 1.8244 1.00 2803 161 0.1888 0.2469 REMARK 3 6 1.8244 - 1.7168 0.99 2849 119 0.1985 0.2829 REMARK 3 7 1.7168 - 1.6308 0.99 2830 139 0.1985 0.2446 REMARK 3 8 1.6308 - 1.5599 0.99 2817 143 0.2154 0.2509 REMARK 3 9 1.5599 - 1.5000 0.98 2727 154 0.2547 0.2537 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.410 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.49 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.12 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 : 0.008 1480 REMARK 3 ANGLE : 0.940 2007 REMARK 3 CHIRALITY : 0.076 213 REMARK 3 PLANARITY : 0.005 262 REMARK 3 DIHEDRAL : 2.153 805 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 7M5A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1000255635. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-AUG-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26921 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.50000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 2VWZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M POTASSIUM SODIUM TARTRATE, 20% REMARK 280 PEG 3350, EVAPORATION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 32.92750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.42350 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 35.69650 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 32.92750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.42350 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 35.69650 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 32.92750 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 35.42350 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 35.69650 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 32.92750 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 35.42350 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 35.69650 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: 1930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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 287 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 321 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 SER A 21 REMARK 465 GLU A 50 REMARK 465 GLY A 51 REMARK 465 VAL A 52 REMARK 465 ALA A 53 REMARK 465 ALA A 54 REMARK 465 PRO A 55 REMARK 465 CYS A 184 REMARK 465 ASN A 185 REMARK 465 GLY A 186 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 ARG A 87 CG CD NE CZ NH1 NH2 DBREF 7M5A A 21 186 UNP Q16611 BAK_HUMAN 21 186 DBREF 7M5A B 80 100 UNP P55957 BID_HUMAN 80 100 SEQADV 7M5A CYS A 184 UNP Q16611 GLY 184 CONFLICT SEQADV 7M5A TRP B 93 UNP P55957 VAL 93 CONFLICT SEQADV 7M5A TRP B 101 UNP P55957 EXPRESSION TAG SEQRES 1 A 166 SER ALA SER GLU GLU GLN VAL ALA GLN ASP THR GLU GLU SEQRES 2 A 166 VAL PHE ARG SER TYR VAL PHE TYR ARG HIS GLN GLN GLU SEQRES 3 A 166 GLN GLU ALA GLU GLY VAL ALA ALA PRO ALA ASP PRO GLU SEQRES 4 A 166 MET VAL THR LEU PRO LEU GLN PRO SER SER THR MET GLY SEQRES 5 A 166 GLN VAL GLY ARG GLN LEU ALA ILE ILE GLY ASP ASP ILE SEQRES 6 A 166 ASN ARG ARG TYR ASP SER GLU PHE GLN THR MET LEU GLN SEQRES 7 A 166 HIS LEU GLN PRO THR ALA GLU ASN ALA TYR GLU TYR PHE SEQRES 8 A 166 THR LYS ILE ALA THR SER LEU PHE GLU SER GLY ILE ASN SEQRES 9 A 166 TRP GLY ARG VAL VAL ALA LEU LEU GLY PHE GLY TYR ARG SEQRES 10 A 166 LEU ALA LEU HIS VAL TYR GLN HIS GLY LEU THR GLY PHE SEQRES 11 A 166 LEU GLY GLN VAL THR ARG PHE VAL VAL ASP PHE MET LEU SEQRES 12 A 166 HIS HIS CYS ILE ALA ARG TRP ILE ALA GLN ARG GLY GLY SEQRES 13 A 166 TRP VAL ALA ALA LEU ASN LEU CYS ASN GLY SEQRES 1 B 22 GLU ASP ILE ILE ARG ASN ILE ALA ARG HIS LEU ALA GLN SEQRES 2 B 22 TRP GLY ASP SER MET ASP ARG SER TRP FORMUL 3 HOH *141(H2 O) HELIX 1 AA1 ALA A 22 ALA A 49 1 28 HELIX 2 AA2 ASP A 57 VAL A 61 5 5 HELIX 3 AA3 THR A 70 GLY A 82 1 13 HELIX 4 AA4 GLY A 82 GLN A 101 1 20 HELIX 5 AA5 ASN A 106 SER A 121 1 16 HELIX 6 AA6 ASN A 124 HIS A 145 1 22 HELIX 7 AA7 PHE A 150 HIS A 165 1 16 HELIX 8 AA8 CYS A 166 ARG A 174 1 9 HELIX 9 AA9 GLY A 175 LEU A 183 5 9 HELIX 10 AB1 ASP B 81 TRP B 101 1 21 SSBOND 1 CYS A 166 CYS A 166 1555 3857 2.07 CRYST1 65.855 70.847 71.393 90.00 90.00 90.00 I 2 2 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 0.015185 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014115 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014007 0.00000