HEADER APOPTOSIS 28-APR-10 3MQP TITLE CRYSTAL STRUCTURE OF HUMAN BFL-1 IN COMPLEX WITH NOXA BH3 PEPTIDE, TITLE 2 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET HR2930 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BCL-2-RELATED PROTEIN A1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BCL-2-LIKE PROTEIN 5, BCL2-L-5, PROTEIN BFL-1, HEMOPOIETIC- COMPND 5 SPECIFIC EARLY RESPONSE PROTEIN, PROTEIN GRS; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: PHORBOL-12-MYRISTATE-13-ACETATE-INDUCED PROTEIN 1; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: NOXA BH3 PEPTIDE, RESIDUES 19-43; COMPND 11 SYNONYM: PMA-INDUCED PROTEIN 1, IMMEDIATE-EARLY-RESPONSE PROTEIN APR, COMPND 12 PROTEIN NOXA; COMPND 13 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)+ MAGIC; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15; 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 SEQUENCE OCCURS NATURALLY IN HUMANS. PEPTIDE WAS SOURCE 17 SYNTHESIZED FROM A COMMERCIAL PEPTIDE SYNTHESIS SERVICE. KEYWDS BCL-2 FAMILY, STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE KEYWDS 2 INITIATIVE, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, NESG, KEYWDS 3 APOPTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR R.GUAN,R.XIAO,L.ZHAO,T.B.ACTON,C.GELINAS,G.T.MONTELIONE,NORTHEAST AUTHOR 2 STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 4 06-SEP-23 3MQP 1 REMARK REVDAT 3 02-APR-14 3MQP 1 SOURCE VERSN REVDAT 2 28-JUL-10 3MQP 1 TITLE REVDAT 1 02-JUN-10 3MQP 0 JRNL AUTH R.GUAN,R.XIAO,L.ZHAO,T.B.ACTON,C.GELINAS,G.T.MONTELIONE JRNL TITL CRYSTAL STRUCTURE OF HUMAN BFL-1 IN COMPLEX WITH NOXA BH3 JRNL TITL 2 PEPTIDE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.24 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_377 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) : 2.24 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.9 REMARK 3 NUMBER OF REFLECTIONS : 7049 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.140 REMARK 3 FREE R VALUE TEST SET COUNT : 715 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : 0.83 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 45.13 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.99 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 3MQP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-MAY-10. REMARK 100 THE DEPOSITION ID IS D_1000058880. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-APR-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.075 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7385 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.240 REMARK 200 RESOLUTION RANGE LOW (A) : 30.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.09300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.38300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.060 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: PDB ENTRY 3I1H REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN SOLUTION: 100MM NACL, 5MM DTT, REMARK 280 0.02% NAN3, 10MM TRIS-HCL (PH 7.5) . RESERVOIR SOLUTION: 1.5 M REMARK 280 SODIUM MALONATE, 0.1 M SODIUM ACETATE, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 296K, PH 4.4 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 21.59800 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: 1920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 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 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 PRO A 26 -135.75 -63.25 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3I1H RELATED DB: PDB REMARK 900 THE SAME HUMAN BFL-1 IN COMPLEX WITH A DIFFERENT BCL-2 BH3 PEPTIDE REMARK 900 RELATED ID: HR2930 RELATED DB: TARGETDB DBREF 3MQP A 1 151 UNP Q16548 B2LA1_HUMAN 1 151 DBREF 3MQP B 19 43 UNP Q13794 APR_HUMAN 19 43 SEQADV 3MQP MET A -9 UNP Q16548 EXPRESSION TAG SEQADV 3MQP GLY A -8 UNP Q16548 EXPRESSION TAG SEQADV 3MQP HIS A -7 UNP Q16548 EXPRESSION TAG SEQADV 3MQP HIS A -6 UNP Q16548 EXPRESSION TAG SEQADV 3MQP HIS A -5 UNP Q16548 EXPRESSION TAG SEQADV 3MQP HIS A -4 UNP Q16548 EXPRESSION TAG SEQADV 3MQP HIS A -3 UNP Q16548 EXPRESSION TAG SEQADV 3MQP HIS A -2 UNP Q16548 EXPRESSION TAG SEQADV 3MQP SER A -1 UNP Q16548 EXPRESSION TAG SEQADV 3MQP 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 CYS 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 25 ALA GLU LEU GLU VAL GLU CYS ALA THR GLN LEU ARG ARG SEQRES 2 B 25 PHE GLY ASP LYS LEU ASN PHE ARG GLN LYS LEU LEU FORMUL 3 HOH *29(H2 O) HELIX 1 1 GLU A 5 GLN A 22 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 PHE A 79 1 17 HELIX 5 5 ASN A 85 GLN A 107 1 23 HELIX 6 6 ASP A 113 ASN A 137 1 25 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 GLU B 20 LYS B 41 1 22 CRYST1 43.138 43.196 46.387 90.00 113.50 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 0.023181 0.000000 0.010080 0.00000 SCALE2 0.000000 0.023150 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023507 0.00000