HEADER DNA BINDING PROTEIN 31-MAY-17 5O55 TITLE CRYSTAL STRUCTURE OF THE HUMAN BRPF1 BROMODOMAIN IN COMPLEX WITH BZ047 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEREGRIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 626-740; COMPND 5 SYNONYM: BROMODOMAIN AND PHD FINGER-CONTAINING PROTEIN 1,PROTEIN COMPND 6 BR140; COMPND 7 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: BRPF1, BR140; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BROMODOMAIN AND PHD FINGER-CONTAINING PROTEIN 1(BRPF1), MONOCYTIC KEYWDS 2 LEUKEMIA ZINC-FINGER (MOZ), INHIBITOR, TRANSCRIPTION, DNA BINDING KEYWDS 3 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.ZHU,A.CAFLISCH REVDAT 3 17-JAN-24 5O55 1 REMARK REVDAT 2 27-JUN-18 5O55 1 JRNL REVDAT 1 13-JUN-18 5O55 0 JRNL AUTH J.ZHU,C.ZHOU,A.CAFLISCH JRNL TITL STRUCTURE-BASED DISCOVERY OF SELECTIVE BRPF1 BROMODOMAIN JRNL TITL 2 INHIBITORS. JRNL REF EUR J MED CHEM V. 155 337 2018 JRNL REFN ISSN 1768-3254 JRNL PMID 29902720 JRNL DOI 10.1016/J.EJMECH.2018.05.037 REMARK 2 REMARK 2 RESOLUTION. 1.45 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 24235 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.270 REMARK 3 FREE R VALUE TEST SET COUNT : 2005 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 27.3576 - 3.4925 0.99 1682 155 0.1662 0.1801 REMARK 3 2 3.4925 - 2.7729 1.00 1623 151 0.1722 0.2032 REMARK 3 3 2.7729 - 2.4227 1.00 1598 141 0.1894 0.2141 REMARK 3 4 2.4227 - 2.2013 1.00 1616 143 0.1782 0.2164 REMARK 3 5 2.2013 - 2.0435 1.00 1579 143 0.1742 0.1848 REMARK 3 6 2.0435 - 1.9231 1.00 1591 144 0.1883 0.2221 REMARK 3 7 1.9231 - 1.8268 1.00 1560 138 0.1816 0.2006 REMARK 3 8 1.8268 - 1.7473 1.00 1594 142 0.1862 0.2290 REMARK 3 9 1.7473 - 1.6800 1.00 1575 143 0.1827 0.2139 REMARK 3 10 1.6800 - 1.6221 1.00 1573 143 0.1862 0.2179 REMARK 3 11 1.6221 - 1.5714 1.00 1570 138 0.1857 0.2185 REMARK 3 12 1.5714 - 1.5264 1.00 1587 144 0.1937 0.2169 REMARK 3 13 1.5264 - 1.4863 1.00 1544 139 0.2084 0.2216 REMARK 3 14 1.4863 - 1.4500 0.97 1538 141 0.2468 0.2852 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.740 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 : 0.008 1040 REMARK 3 ANGLE : 0.755 1410 REMARK 3 CHIRALITY : 0.062 146 REMARK 3 PLANARITY : 0.004 187 REMARK 3 DIHEDRAL : 11.702 1103 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 15.2755 -22.5521 0.4271 REMARK 3 T TENSOR REMARK 3 T11: 0.1884 T22: 0.1969 REMARK 3 T33: 0.1540 T12: -0.0809 REMARK 3 T13: -0.0148 T23: 0.0073 REMARK 3 L TENSOR REMARK 3 L11: 2.1086 L22: 3.4780 REMARK 3 L33: 1.9893 L12: -1.1933 REMARK 3 L13: 0.9628 L23: -1.2402 REMARK 3 S TENSOR REMARK 3 S11: 0.0042 S12: -0.1600 S13: -0.1218 REMARK 3 S21: 0.2830 S22: -0.0291 S23: 0.0654 REMARK 3 S31: -0.0175 S32: -0.0944 S33: -0.0056 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 5O55 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-JUN-17. REMARK 100 THE DEPOSITION ID IS D_1200005200. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-OCT-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 : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.999989 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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: 4LC2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PROPANE, PH6.5, 0.15 M REMARK 280 SODIUM NITRATE, 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.09800 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 21.04900 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 21.04900 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 42.09800 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 1.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 987 LIES ON A SPECIAL POSITION. 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 SER A 625 REMARK 465 MET A 626 REMARK 465 GLY A 740 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 LYS A 670 CD CE NZ REMARK 470 GLN A 731 CD OE1 NE2 REMARK 470 LYS A 738 CE NZ 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 1039 O HOH A 1040 1.85 REMARK 500 O HOH A 1005 O HOH A 1032 1.91 REMARK 500 O HOH A 1039 O HOH A 1043 1.94 REMARK 500 O HOH A 1040 O HOH A 1043 2.12 REMARK 500 O HOH A 923 O HOH A 1009 2.13 REMARK 500 O HOH A 1041 O HOH A 1042 2.16 REMARK 500 O HOH A 910 O HOH A 1012 2.17 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 A1039 DISTANCE = 6.05 ANGSTROMS REMARK 525 HOH A1040 DISTANCE = 6.54 ANGSTROMS REMARK 525 HOH A1041 DISTANCE = 6.67 ANGSTROMS REMARK 525 HOH A1042 DISTANCE = 6.67 ANGSTROMS REMARK 525 HOH A1043 DISTANCE = 6.84 ANGSTROMS REMARK 525 HOH A1044 DISTANCE = 7.15 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO3 A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9L5 A 802 DBREF 5O55 A 626 740 UNP P55201 BRPF1_HUMAN 626 740 SEQADV 5O55 SER A 625 UNP P55201 EXPRESSION TAG SEQRES 1 A 116 SER MET GLU MET GLN LEU THR PRO PHE LEU ILE LEU LEU SEQRES 2 A 116 ARG LYS THR LEU GLU GLN LEU GLN GLU LYS ASP THR GLY SEQRES 3 A 116 ASN ILE PHE SER GLU PRO VAL PRO LEU SER GLU VAL PRO SEQRES 4 A 116 ASP TYR LEU ASP HIS ILE LYS LYS PRO MET ASP PHE PHE SEQRES 5 A 116 THR MET LYS GLN ASN LEU GLU ALA TYR ARG TYR LEU ASN SEQRES 6 A 116 PHE ASP ASP PHE GLU GLU ASP PHE ASN LEU ILE VAL SER SEQRES 7 A 116 ASN CYS LEU LYS TYR ASN ALA LYS ASP THR ILE PHE TYR SEQRES 8 A 116 ARG ALA ALA VAL ARG LEU ARG GLU GLN GLY GLY ALA VAL SEQRES 9 A 116 LEU ARG GLN ALA ARG ARG GLN ALA GLU LYS MET GLY HET NO3 A 801 4 HET 9L5 A 802 26 HETNAM NO3 NITRATE ION HETNAM 9L5 ~{N}-[(1~{S})-1-(1,5-DIMETHYLPYRAZOL-4-YL)ETHYL]-1- HETNAM 2 9L5 ETHYL-3-METHYL-2-OXIDANYLIDENE-QUINOXALINE-6- HETNAM 3 9L5 CARBOXAMIDE FORMUL 2 NO3 N O3 1- FORMUL 3 9L5 C19 H23 N5 O2 FORMUL 4 HOH *144(H2 O) HELIX 1 AA1 GLN A 629 ASP A 648 1 20 HELIX 2 AA2 ASP A 664 ILE A 669 1 6 HELIX 3 AA3 ASP A 674 ALA A 684 1 11 HELIX 4 AA4 ASN A 689 ASN A 708 1 20 HELIX 5 AA5 THR A 712 MET A 739 1 28 SITE 1 AC1 6 SER A 702 LEU A 705 LYS A 706 TYR A 715 SITE 2 AC1 6 ARG A 722 HOH A 909 SITE 1 AC2 9 ILE A 652 VAL A 657 PRO A 658 VAL A 662 SITE 2 AC2 9 TYR A 707 ASN A 708 PHE A 714 LYS A 738 SITE 3 AC2 9 HOH A 911 CRYST1 60.695 60.695 63.147 90.00 90.00 120.00 P 32 2 1 6 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 0.016476 0.009512 0.000000 0.00000 SCALE2 0.000000 0.019025 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015836 0.00000