HEADER APOPTOSIS 20-FEB-23 8IGC TITLE CRYSTAL STRUCTURE OF BAK BOUND TO BNIP5 BH3 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 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: PROTEIN BNIP5; COMPND 9 CHAIN: B; 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; 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 BCL-2-INTERACTING PROTEIN 5, BNIP5, BAK, BH3, APOPTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR B.KU,D.LIM REVDAT 2 27-DEC-23 8IGC 1 JRNL REVDAT 1 20-SEP-23 8IGC 0 JRNL AUTH D.LIM,D.E.JEONG,H.C.SHIN,J.S.CHOI,J.SEO,S.J.KIM,B.KU JRNL TITL CRYSTAL STRUCTURE OF BAK BOUND TO THE BH3 DOMAIN OF BNIP5, A JRNL TITL 2 NONCANONICAL BH3 DOMAIN-CONTAINING PROTEIN. JRNL REF PROTEINS V. 92 44 2024 JRNL REFN ESSN 1097-0134 JRNL PMID 37553948 JRNL DOI 10.1002/PROT.26568 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 25531 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.830 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 27.4000 - 4.0848 0.81 1506 128 0.2084 0.2244 REMARK 3 2 4.0848 - 3.2439 0.95 1678 143 0.1697 0.2102 REMARK 3 3 3.2439 - 2.8343 0.99 1747 148 0.2117 0.2269 REMARK 3 4 2.8343 - 2.5754 0.99 1723 147 0.2066 0.2370 REMARK 3 5 2.5754 - 2.3909 0.99 1738 147 0.2016 0.2017 REMARK 3 6 2.3909 - 2.2500 0.99 1702 145 0.1990 0.1970 REMARK 3 7 2.2500 - 2.1374 0.99 1698 144 0.2027 0.2235 REMARK 3 8 2.1374 - 2.0444 0.98 1690 144 0.2065 0.2353 REMARK 3 9 2.0444 - 1.9657 0.98 1712 145 0.2147 0.2409 REMARK 3 10 1.9657 - 1.8979 0.99 1682 143 0.2056 0.2524 REMARK 3 11 1.8979 - 1.8385 0.97 1674 143 0.2220 0.2345 REMARK 3 12 1.8385 - 1.7860 0.97 1684 142 0.2452 0.3017 REMARK 3 13 1.7860 - 1.7390 0.99 1679 143 0.2451 0.2740 REMARK 3 14 1.7390 - 1.6970 0.94 1618 138 0.2716 0.2921 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.040 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 : 0.006 1440 REMARK 3 ANGLE : 0.755 1950 REMARK 3 CHIRALITY : 0.050 213 REMARK 3 PLANARITY : 0.005 251 REMARK 3 DIHEDRAL : 14.534 839 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 8IGC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1300035622. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-OCT-22 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25537 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.697 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 (%) : 96.5 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 49.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.7 M SODIUM CITRATE TRIBASIC REMARK 280 DEHYDRATE AND 0.1 M TRIS-HCL (PH 8.5), VAPOR DIFFUSION, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z 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 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 20.88950 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 20.88950 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 44.36800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 63.10600 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 44.36800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 63.10600 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 20.88950 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 44.36800 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 63.10600 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 20.88950 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 44.36800 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 63.10600 REMARK 290 SMTRY3 8 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: 2200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 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 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 GLY A 20 REMARK 465 SER A 21 REMARK 465 GLU A 48 REMARK 465 ALA A 49 REMARK 465 GLU A 50 REMARK 465 GLY A 51 REMARK 465 VAL A 52 REMARK 465 ALA A 53 REMARK 465 THR A 148 REMARK 465 GLY A 149 REMARK 465 LEU B 267 REMARK 465 ALA B 268 REMARK 465 SER B 269 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 GLN A 47 CD OE1 NE2 REMARK 470 ARG A 87 CD NE CZ NH1 NH2 REMARK 470 ARG A 88 CD NE CZ NH1 NH2 REMARK 470 GLU A 92 CD OE1 OE2 REMARK 470 GLU A 120 CD OE1 OE2 REMARK 470 LEU A 147 CG CD1 CD2 REMARK 470 ARG A 169 NE CZ NH1 NH2 REMARK 470 ASP B 244 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 SER A 166 17.69 82.94 REMARK 500 REMARK 500 REMARK: NULL DBREF 8IGC A 23 183 UNP Q16611 BAK_HUMAN 23 183 DBREF 8IGC B 244 269 UNP P0C671 BNIP5_HUMAN 244 269 SEQADV 8IGC GLY A 20 UNP Q16611 EXPRESSION TAG SEQADV 8IGC SER A 21 UNP Q16611 EXPRESSION TAG SEQADV 8IGC MET A 22 UNP Q16611 EXPRESSION TAG SEQADV 8IGC SER A 166 UNP Q16611 CYS 166 ENGINEERED MUTATION SEQRES 1 A 164 GLY SER MET SER GLU GLU GLN VAL ALA GLN ASP THR GLU SEQRES 2 A 164 GLU VAL PHE ARG SER TYR VAL PHE TYR ARG HIS GLN GLN SEQRES 3 A 164 GLU GLN GLU ALA GLU GLY VAL ALA ALA PRO ALA ASP PRO SEQRES 4 A 164 GLU MET VAL THR LEU PRO LEU GLN PRO SER SER THR MET SEQRES 5 A 164 GLY GLN VAL GLY ARG GLN LEU ALA ILE ILE GLY ASP ASP SEQRES 6 A 164 ILE ASN ARG ARG TYR ASP SER GLU PHE GLN THR MET LEU SEQRES 7 A 164 GLN HIS LEU GLN PRO THR ALA GLU ASN ALA TYR GLU TYR SEQRES 8 A 164 PHE THR LYS ILE ALA THR SER LEU PHE GLU SER GLY ILE SEQRES 9 A 164 ASN TRP GLY ARG VAL VAL ALA LEU LEU GLY PHE GLY TYR SEQRES 10 A 164 ARG LEU ALA LEU HIS VAL TYR GLN HIS GLY LEU THR GLY SEQRES 11 A 164 PHE LEU GLY GLN VAL THR ARG PHE VAL VAL ASP PHE MET SEQRES 12 A 164 LEU HIS HIS SER ILE ALA ARG TRP ILE ALA GLN ARG GLY SEQRES 13 A 164 GLY TRP VAL ALA ALA LEU ASN LEU SEQRES 1 B 26 ASP ALA ILE ILE GLN MET ILE VAL GLU LEU LEU LYS ARG SEQRES 2 B 26 VAL GLY ASP GLN TRP GLU GLU GLU GLN SER LEU ALA SER FORMUL 3 HOH *126(H2 O) HELIX 1 AA1 SER A 23 GLU A 46 1 24 HELIX 2 AA2 PRO A 58 LEU A 63 1 6 HELIX 3 AA3 SER A 69 GLN A 101 1 33 HELIX 4 AA4 ASN A 106 PHE A 119 1 14 HELIX 5 AA5 ASN A 124 GLY A 146 1 23 HELIX 6 AA6 LEU A 151 HIS A 165 1 15 HELIX 7 AA7 SER A 166 ARG A 174 1 9 HELIX 8 AA8 GLY A 175 ASN A 182 5 8 HELIX 9 AA9 ALA B 245 SER B 266 1 22 CRYST1 88.736 126.212 41.779 90.00 90.00 90.00 C 2 2 21 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 0.011269 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007923 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023935 0.00000