HEADER APOPTOSIS 17-FEB-17 5UUL TITLE HUMAN BFL-1 IN COMPLEX WITH PUMA BH3 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: BCL-2-BINDING COMPONENT 3; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: UNP RESIDUES 132-154; COMPND 12 SYNONYM: JFY-1,P53 UP-REGULATED MODULATOR OF APOPTOSIS; 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: 562; 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 APOPTOSIS REGULATORY PROTEINS, PROTEIN BINDING, PROTEIN STRUCTURE, KEYWDS 2 PROTO-ONCOGENE, BCL2A1, BCL2 RELATED PROTEIN A1, APOPTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR J.M.JENSON,R.A.GRANT,A.E.KEATING REVDAT 4 04-OCT-23 5UUL 1 REMARK REVDAT 3 01-JAN-20 5UUL 1 REMARK REVDAT 2 27-SEP-17 5UUL 1 REMARK REVDAT 1 21-JUN-17 5UUL 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. 1.33 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10_2155 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) : 1.33 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 35887 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.134 REMARK 3 R VALUE (WORKING SET) : 0.133 REMARK 3 FREE R VALUE : 0.155 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.610 REMARK 3 FREE R VALUE TEST SET COUNT : 2013 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 43.1766 - 3.2053 0.99 2540 154 0.1591 0.1725 REMARK 3 2 3.2053 - 2.5442 0.99 2472 150 0.1524 0.1417 REMARK 3 3 2.5442 - 2.2226 1.00 2514 147 0.1225 0.1393 REMARK 3 4 2.2226 - 2.0194 0.99 2474 148 0.1171 0.1315 REMARK 3 5 2.0194 - 1.8747 0.99 2458 146 0.1125 0.1415 REMARK 3 6 1.8747 - 1.7641 0.99 2466 140 0.1106 0.1725 REMARK 3 7 1.7641 - 1.6758 1.00 2468 154 0.1050 0.1497 REMARK 3 8 1.6758 - 1.6028 1.00 2455 146 0.0997 0.1385 REMARK 3 9 1.6028 - 1.5411 1.00 2476 148 0.0981 0.1589 REMARK 3 10 1.5411 - 1.4880 1.00 2457 148 0.1098 0.1558 REMARK 3 11 1.4880 - 1.4414 1.00 2487 136 0.1123 0.1607 REMARK 3 12 1.4414 - 1.4002 0.99 2418 154 0.1198 0.1890 REMARK 3 13 1.4002 - 1.3634 0.94 2317 135 0.1439 0.1758 REMARK 3 14 1.3634 - 1.3301 0.75 1872 107 0.1692 0.2385 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.510 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.07 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.83 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 1544 REMARK 3 ANGLE : 0.778 2102 REMARK 3 CHIRALITY : 0.070 224 REMARK 3 PLANARITY : 0.005 277 REMARK 3 DIHEDRAL : 12.080 609 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 5UUL 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_1000226490. 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 : 7.0 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 : 35909 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.330 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 (%) : 97.6 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.33 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.28000 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: PHASER REMARK 200 STARTING MODEL: 4ZEQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.45 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 21.71400 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: 2320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.0 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 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 271 O HOH A 308 1.88 REMARK 500 O HOH A 267 O HOH A 310 2.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 HH21 ARG B 12 O HOH A 312 2444 1.60 REMARK 500 O3 SO4 B 101 O HOH A 308 1545 1.94 REMARK 500 O2 SO4 B 101 O HOH A 238 1545 1.98 REMARK 500 O1 SO4 B 101 O HOH A 308 1545 2.07 REMARK 500 O HOH A 283 O HOH B 216 2454 2.11 REMARK 500 NH2 ARG B 12 O HOH A 312 2444 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 329 DISTANCE = 6.50 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5UUK RELATED DB: PDB REMARK 900 RELATED ID: 5UUM RELATED DB: PDB REMARK 900 RELATED ID: 5UUP RELATED DB: PDB DBREF 5UUL A 1 151 UNP Q16548 B2LA1_HUMAN 1 151 DBREF 5UUL B 1 23 UNP Q9BXH1 BBC3_HUMAN 132 154 SEQADV 5UUL GLY A 0 UNP Q16548 EXPRESSION TAG SEQADV 5UUL ACE B 0 UNP Q9BXH1 ACETYLATION SEQADV 5UUL NH2 B 24 UNP Q9BXH1 AMIDATION 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 25 ACE GLN TRP ALA ARG GLU ILE GLY ALA GLN LEU ARG ARG SEQRES 2 B 25 MET ALA ASP ASP LEU ASN ALA GLN TYR GLU ARG NH2 HET ACE B 0 6 HET NH2 B 24 3 HET SO4 B 101 5 HETNAM ACE ACETYL GROUP HETNAM NH2 AMINO GROUP HETNAM SO4 SULFATE ION FORMUL 2 ACE C2 H4 O FORMUL 2 NH2 H2 N FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *147(H2 O) HELIX 1 AA1 GLU A 5 GLN A 22 1 18 HELIX 2 AA2 SER A 31 LEU A 52 1 22 HELIX 3 AA3 LEU A 52 ASN A 58 1 7 HELIX 4 AA4 SER A 63 PHE A 79 1 17 HELIX 5 AA5 ASN A 85 GLN A 107 1 23 HELIX 6 AA6 ASP A 113 ASN A 137 1 25 HELIX 7 AA7 GLY A 138 GLY A 143 1 6 HELIX 8 AA8 GLY A 143 GLU A 149 1 7 HELIX 9 AA9 GLN B 1 GLN B 20 1 20 LINK C ACE B 0 N GLN B 1 1555 1555 1.37 LINK C ARG B 23 N NH2 B 24 1555 1555 1.34 SITE 1 AC1 9 SER A 63 VAL A 64 GLN A 107 ALA A 109 SITE 2 AC1 9 HOH A 238 HOH A 277 HOH A 308 HOH A 325 SITE 3 AC1 9 ARG B 23 CRYST1 43.213 43.428 47.384 90.00 114.39 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 0.023141 0.000000 0.010494 0.00000 SCALE2 0.000000 0.023027 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023173 0.00000