HEADER APOPTOSIS 17-FEB-17 5UUP TITLE HUMAN BFL-1 COVALENTLY CROSS-LINKED TO AN ELECTROPHILIC VARIANT OF A TITLE 2 BFL-1-SPECIFIC SELECTED PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BCL-2-RELATED PROTEIN A1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-151; COMPND 5 SYNONYM: BCL-2-LIKE PROTEIN 5,BCL2-L-5,HEMOPOIETIC-SPECIFIC EARLY COMPND 6 RESPONSE PROTEIN,PROTEIN BFL-1,PROTEIN GRS; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: BFL-1-SPECIFIC SELECTED PEPTIDE; COMPND 10 CHAIN: B; COMPND 11 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: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630 KEYWDS APOPTOSIS REGULATORY PROTEINS, ELECTROPHILE, PROTEIN BINDING, PROTEIN KEYWDS 2 STRUCTURE, PROTO-ONCOGENE, SPECIFICITY, BCL2A1, BCL2 RELATED PROTEIN KEYWDS 3 A1, PEPTIDE INHIBITOR, APOPTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR J.M.JENSON,R.A.GRANT,A.E.KEATING REVDAT 4 04-OCT-23 5UUP 1 REMARK REVDAT 3 01-JAN-20 5UUP 1 REMARK REVDAT 2 27-SEP-17 5UUP 1 REMARK REVDAT 1 21-JUN-17 5UUP 0 JRNL AUTH J.M.JENSON,J.A.RYAN,R.A.GRANT,A.LETAI,A.E.KEATING JRNL TITL EPISTATIC MUTATIONS IN PUMA BH3 DRIVE AN ALTERNATE BINDING JRNL TITL 2 MODE TO POTENTLY AND SELECTIVELY INHIBIT ANTI-APOPTOTIC JRNL TITL 3 BFL-1. JRNL REF ELIFE V. 6 2017 JRNL REFN ESSN 2050-084X JRNL PMID 28594323 JRNL DOI 10.7554/ELIFE.25541 REMARK 2 REMARK 2 RESOLUTION. 1.73 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.73 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 3 NUMBER OF REFLECTIONS : 15887 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.090 REMARK 3 FREE R VALUE TEST SET COUNT : 1603 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 39.4090 - 3.8382 0.99 1417 156 0.1666 0.1732 REMARK 3 2 3.8382 - 3.0469 0.99 1385 156 0.1633 0.1851 REMARK 3 3 3.0469 - 2.6618 1.00 1385 157 0.1741 0.2020 REMARK 3 4 2.6618 - 2.4185 0.99 1375 147 0.1714 0.1945 REMARK 3 5 2.4185 - 2.2452 1.00 1387 155 0.1700 0.2109 REMARK 3 6 2.2452 - 2.1128 1.00 1350 160 0.1795 0.1953 REMARK 3 7 2.1128 - 2.0070 0.99 1372 149 0.1960 0.2577 REMARK 3 8 2.0070 - 1.9196 0.99 1365 149 0.2079 0.2450 REMARK 3 9 1.9196 - 1.8457 0.96 1320 147 0.2300 0.2671 REMARK 3 10 1.8457 - 1.7820 0.85 1153 139 0.2735 0.3532 REMARK 3 11 1.7820 - 1.7263 0.57 775 88 0.3157 0.3360 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 22.960 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.46 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.57 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 1460 REMARK 3 ANGLE : 0.484 1973 REMARK 3 CHIRALITY : 0.041 214 REMARK 3 PLANARITY : 0.003 258 REMARK 3 DIHEDRAL : 9.867 879 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 5UUP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-FEB-17. REMARK 100 THE DEPOSITION ID IS D_1000226493. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUN-16 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 : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : .97920 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15904 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.726 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.73 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 51.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.30300 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: 4ZEQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8 M AMMONIUM SULFATE, 0.1 M MES PH REMARK 280 7.0, 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 21.74650 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 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 NH2 B 24 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 O HOH A 308 O HOH A 391 2.08 REMARK 500 NH2 ARG B 23 O HOH B 101 2.14 REMARK 500 O HOH A 383 O HOH A 393 2.14 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 ALA A 109 78.37 -113.28 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5UUK RELATED DB: PDB REMARK 900 RELATED ID: 5UUL RELATED DB: PDB REMARK 900 RELATED ID: 5UUM RELATED DB: PDB DBREF 5UUP A 1 151 UNP Q16548 B2LA1_HUMAN 1 151 DBREF 5UUP B 1 24 PDB 5UUP 5UUP 1 24 SEQADV 5UUP GLY A 0 UNP Q16548 EXPRESSION TAG SEQRES 1 A 152 GLY MET THR ASP CYS GLU PHE GLY TYR ILE TYR ARG LEU SEQRES 2 A 152 ALA GLN ASP TYR LEU GLN CYS VAL LEU GLN ILE PRO GLN SEQRES 3 A 152 PRO GLY SER GLY PRO SER LYS THR SER ARG VAL LEU GLN SEQRES 4 A 152 ASN VAL ALA PHE SER VAL GLN LYS GLU VAL GLU LYS ASN SEQRES 5 A 152 LEU LYS SER CYS LEU ASP ASN VAL ASN VAL VAL SER VAL SEQRES 6 A 152 ASP THR ALA ARG THR LEU PHE ASN GLN VAL MET GLU LYS SEQRES 7 A 152 GLU PHE GLU ASP GLY ILE ILE ASN TRP GLY ARG ILE VAL SEQRES 8 A 152 THR ILE PHE ALA PHE GLU GLY ILE LEU ILE LYS LYS LEU SEQRES 9 A 152 LEU ARG GLN GLN ILE ALA PRO ASP VAL ASP THR TYR LYS SEQRES 10 A 152 GLU ILE SER TYR PHE VAL ALA GLU PHE ILE MET ASN ASN SEQRES 11 A 152 THR GLY GLU TRP ILE ARG GLN ASN GLY GLY TRP GLU ASN SEQRES 12 A 152 GLY PHE VAL LYS LYS PHE GLU PRO LYS SEQRES 1 B 24 AKR GLY VAL ARG GLU ILE ALA TYR GLY LEU ARG ARG ALA SEQRES 2 B 24 ALA ASP ASP VAL ASN ALA GLN VAL GLU ARG NH2 HET AKR B 1 8 HET SO4 A 201 5 HET SO4 A 202 5 HETNAM AKR ACRYLIC ACID HETNAM SO4 SULFATE ION FORMUL 2 AKR C3 H4 O2 FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 HOH *120(H2 O) HELIX 1 AA1 GLY A 0 CYS A 4 5 5 HELIX 2 AA2 GLU A 5 LEU A 21 1 17 HELIX 3 AA3 SER A 31 LEU A 52 1 22 HELIX 4 AA4 LEU A 52 ASN A 58 1 7 HELIX 5 AA5 SER A 63 GLU A 80 1 18 HELIX 6 AA6 ASN A 85 GLN A 107 1 23 HELIX 7 AA7 ASP A 113 ASN A 137 1 25 HELIX 8 AA8 GLY A 138 GLY A 143 1 6 HELIX 9 AA9 GLY A 143 GLU A 149 1 7 HELIX 10 AB1 GLY B 2 GLN B 20 1 19 LINK SG CYS A 55 CB AKR B 1 1555 1555 1.79 LINK C AKR B 1 N GLY B 2 1555 1555 1.34 SITE 1 AC1 4 TYR A 10 ARG A 11 GLN A 14 LYS A 116 SITE 1 AC2 2 ARG A 105 GLN A 106 CRYST1 43.395 43.493 47.068 90.00 114.78 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 0.023044 0.000000 0.010639 0.00000 SCALE2 0.000000 0.022992 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023401 0.00000