HEADER APOPTOSIS 26-JUN-09 3I1H TITLE CRYSTAL STRUCTURE OF HUMAN BFL-1 IN COMPLEX WITH BAK BH3 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN BFL-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-151; COMPND 5 SYNONYM: BCL-2-LIKE PROTEIN 5, BCL2-L-5, BCL-2-RELATED PROTEIN A1, COMPND 6 HEMOPOIETIC-SPECIFIC EARLY RESPONSE PROTEIN, PROTEIN GRS; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: APOPTOSIS REGULATOR BAK; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: BH3; COMPND 12 SYNONYM: BCL-2 HOMOLOGOUS ANTAGONIST/KILLER, BCL-2-LIKE PROTEIN 7, COMPND 13 BCL2-L-7; COMPND 14 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: BCL2A1, BCL2L5, BFL1, GRS, HBPA1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 DE3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B; 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 PEPTIDE WAS SYNTHESIZED. KEYWDS BCL-2 FAMILY, BFL-1, BAK BH3, COMPLEX, APOPTOSIS, PRO-SURVIVAL KEYWDS 2 PROTEIN, STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE INITIATIVE, KEYWDS 3 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, NESG, MEMBRANE, METAL- KEYWDS 4 BINDING, TRANSMEMBRANE EXPDTA X-RAY DIFFRACTION AUTHOR R.GUAN,R.XIAO,L.ZHAO,T.ACTON,E.WHITE,C.GELINAS,G.T.MONTELIONE, AUTHOR 2 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 3 06-SEP-23 3I1H 1 LINK REVDAT 2 12-NOV-14 3I1H 1 HET HETATM HETNAM HETSYN REVDAT 2 2 1 LINK MODRES SEQRES VERSN REVDAT 1 14-JUL-09 3I1H 0 JRNL AUTH R.GUAN,R.XIAO,L.ZHAO,T.ACTON,E.WHITE,C.GELINAS, JRNL AUTH 2 G.T.MONTELIONE JRNL TITL CRYSTAL STRUCTURE OF HUMAN BFL-1 IN COMPLEX WITH BAK BH3 JRNL TITL 2 PEPTIDE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.07 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 785414.930 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 7957 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 SET) : 0.213 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.400 REMARK 3 FREE R VALUE TEST SET COUNT : 427 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.012 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1245 REMARK 3 BIN R VALUE (WORKING SET) : 0.2590 REMARK 3 BIN FREE R VALUE : 0.2910 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 65 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.036 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1284 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 31 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.31000 REMARK 3 B22 (A**2) : -7.55000 REMARK 3 B33 (A**2) : 8.87000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -8.96000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.27 REMARK 3 ESD FROM SIGMAA (A) : 0.22 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.32 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.25 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 17.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.910 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : GROUP 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 43.40 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 3I1H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000053844. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-OCT-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97893 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7958 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 30.070 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.46 REMARK 200 R MERGE FOR SHELL (I) : 0.34200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 2VOH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5 M SODIUM MALONATE, PH 5.8 PROTEIN REMARK 280 1.67 MG/ML, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 21.57250 REMARK 290 SMTRY3 2 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: 1450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 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 MET A -9 REMARK 465 GLY A -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 THR A 2 REMARK 465 ASP A 3 REMARK 465 GLN A 25 REMARK 465 PRO A 26 REMARK 465 GLY A 27 REMARK 465 SER A 28 REMARK 465 GLY A 29 REMARK 465 LYS A 151 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NE2 GLN A 14 O HOH A 176 1.16 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 GLU A 5 -72.27 -43.90 REMARK 500 LYS A 53 -79.04 -39.39 REMARK 500 PRO A 110 79.94 -49.93 REMARK 500 VAL A 112 21.01 -57.84 REMARK 500 ASP A 113 40.68 -140.59 REMARK 500 GLN B 73 -139.61 48.35 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HR2930 RELATED DB: TARGETDB DBREF 3I1H A 1 151 UNP Q16548 B2LA1_HUMAN 1 151 DBREF 3I1H B 72 87 UNP Q16611 BAK_HUMAN 72 87 SEQADV 3I1H MET A -9 UNP Q16548 EXPRESSION TAG SEQADV 3I1H GLY A -8 UNP Q16548 EXPRESSION TAG SEQADV 3I1H HIS A -7 UNP Q16548 EXPRESSION TAG SEQADV 3I1H HIS A -6 UNP Q16548 EXPRESSION TAG SEQADV 3I1H HIS A -5 UNP Q16548 EXPRESSION TAG SEQADV 3I1H HIS A -4 UNP Q16548 EXPRESSION TAG SEQADV 3I1H HIS A -3 UNP Q16548 EXPRESSION TAG SEQADV 3I1H HIS A -2 UNP Q16548 EXPRESSION TAG SEQADV 3I1H SER A -1 UNP Q16548 EXPRESSION TAG SEQADV 3I1H HIS A 0 UNP Q16548 EXPRESSION TAG SEQRES 1 A 161 MET GLY HIS HIS HIS HIS HIS HIS SER HIS MET THR ASP SEQRES 2 A 161 CYS GLU PHE GLY TYR ILE TYR ARG LEU ALA GLN ASP TYR SEQRES 3 A 161 LEU GLN CSD VAL LEU GLN ILE PRO GLN PRO GLY SER GLY SEQRES 4 A 161 PRO SER LYS THR SER ARG VAL LEU GLN ASN VAL ALA PHE SEQRES 5 A 161 SER VAL GLN LYS GLU VAL GLU LYS ASN LEU LYS SER CYS SEQRES 6 A 161 LEU ASP ASN VAL ASN VAL VAL SER VAL ASP THR ALA ARG SEQRES 7 A 161 THR LEU PHE ASN GLN VAL MET GLU LYS GLU PHE GLU ASP SEQRES 8 A 161 GLY ILE ILE ASN TRP GLY ARG ILE VAL THR ILE PHE ALA SEQRES 9 A 161 PHE GLU GLY ILE LEU ILE LYS LYS LEU LEU ARG GLN GLN SEQRES 10 A 161 ILE ALA PRO ASP VAL ASP THR TYR LYS GLU ILE SER TYR SEQRES 11 A 161 PHE VAL ALA GLU PHE ILE MET ASN ASN THR GLY GLU TRP SEQRES 12 A 161 ILE ARG GLN ASN GLY GLY TRP GLU ASN GLY PHE VAL LYS SEQRES 13 A 161 LYS PHE GLU PRO LYS SEQRES 1 B 16 GLY GLN VAL GLY ARG GLN LEU ALA ILE ILE GLY ASP ASP SEQRES 2 B 16 ILE ASN ARG MODRES 3I1H CSD A 19 CYS 3-SULFINOALANINE HET CSD A 19 8 HETNAM CSD 3-SULFINOALANINE HETSYN CSD S-CYSTEINESULFINIC ACID; S-SULFINOCYSTEINE FORMUL 1 CSD C3 H7 N O4 S FORMUL 3 HOH *31(H2 O) HELIX 1 1 CYS A 4 LEU A 21 1 18 HELIX 2 2 SER A 31 LEU A 52 1 22 HELIX 3 3 LEU A 52 ASN A 58 1 7 HELIX 4 4 SER A 63 GLU A 80 1 18 HELIX 5 5 ASN A 85 GLN A 107 1 23 HELIX 6 6 THR A 114 ASN A 137 1 24 HELIX 7 7 GLY A 138 GLY A 143 1 6 HELIX 8 8 GLY A 143 GLU A 149 1 7 HELIX 9 9 GLY B 72 ARG B 87 1 16 LINK C GLN A 18 N CSD A 19 1555 1555 1.33 LINK C CSD A 19 N VAL A 20 1555 1555 1.33 CRYST1 43.236 43.145 46.068 90.00 114.45 90.00 P 1 21 1 2 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 0.023129 0.000000 0.010516 0.00000 SCALE2 0.000000 0.023178 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023845 0.00000