HEADER DNA BINDING PROTEIN 20-JAN-17 5MWZ TITLE CRYSTAL STRUCTURE OF THE HUMAN BRPF1 BROMODOMAIN IN COMPLEX WITH BZ073 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEREGRIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BROMODOMAIN AND PHD FINGER-CONTAINING PROTEIN 1,PROTEIN COMPND 5 BR140; COMPND 6 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 16-OCT-19 5MWZ 1 REMARK REVDAT 2 27-JUN-18 5MWZ 1 JRNL REVDAT 1 14-FEB-18 5MWZ 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. 1.25 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) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 37798 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.181 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.320 REMARK 3 FREE R VALUE TEST SET COUNT : 2010 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 40.4814 - 3.0123 1.00 2700 151 0.1661 0.1742 REMARK 3 2 3.0123 - 2.3911 1.00 2613 147 0.1734 0.1959 REMARK 3 3 2.3911 - 2.0888 1.00 2561 147 0.1616 0.1653 REMARK 3 4 2.0888 - 1.8979 1.00 2576 142 0.1581 0.2001 REMARK 3 5 1.8979 - 1.7618 1.00 2552 145 0.1652 0.1915 REMARK 3 6 1.7618 - 1.6579 1.00 2543 135 0.1556 0.1946 REMARK 3 7 1.6579 - 1.5749 1.00 2542 144 0.1542 0.1832 REMARK 3 8 1.5749 - 1.5064 1.00 2543 139 0.1507 0.1810 REMARK 3 9 1.5064 - 1.4484 1.00 2539 141 0.1552 0.1624 REMARK 3 10 1.4484 - 1.3984 1.00 2545 146 0.1649 0.1692 REMARK 3 11 1.3984 - 1.3547 1.00 2503 144 0.1662 0.1884 REMARK 3 12 1.3547 - 1.3159 1.00 2532 142 0.1640 0.1631 REMARK 3 13 1.3159 - 1.2813 1.00 2519 145 0.1669 0.1729 REMARK 3 14 1.2813 - 1.2500 1.00 2520 142 0.1650 0.1869 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) : 0.070 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.730 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 : 0.004 1014 REMARK 3 ANGLE : 0.768 1373 REMARK 3 CHIRALITY : 0.066 143 REMARK 3 PLANARITY : 0.006 178 REMARK 3 DIHEDRAL : 11.065 656 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): -14.8917 23.3194 0.8872 REMARK 3 T TENSOR REMARK 3 T11: 0.0874 T22: 0.0783 REMARK 3 T33: 0.0772 T12: -0.0148 REMARK 3 T13: 0.0057 T23: -0.0026 REMARK 3 L TENSOR REMARK 3 L11: 0.6106 L22: 0.9410 REMARK 3 L33: 0.6370 L12: -0.1821 REMARK 3 L13: -0.2947 L23: 0.4598 REMARK 3 S TENSOR REMARK 3 S11: 0.0178 S12: -0.0361 S13: 0.0658 REMARK 3 S21: 0.0302 S22: 0.0006 S23: -0.0659 REMARK 3 S31: -0.0295 S32: 0.0346 S33: 0.0006 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 5MWZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-JAN-17. REMARK 100 THE DEPOSITION ID IS D_1200003146. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-AUG-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 : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000019 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 : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37830 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 40.460 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 18.40 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 31.4000 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: NULL REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PROPANE PH7.4, 25% REMARK 280 PEG3350, 5% EG, 0.15 M NANO3, VAPOR DIFFUSION, SITTING 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 42.13800 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 21.06900 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 21.06900 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 42.13800 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: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 A1007 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1022 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 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 LYS A 706 CE NZ REMARK 470 GLN A 731 CG CD OE1 NE2 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 1021 O HOH A 1063 1.86 REMARK 500 O HOH A 1104 O HOH A 1109 1.98 REMARK 500 O HOH A 1055 O HOH A 1068 2.05 REMARK 500 O HOH A 992 O HOH A 1032 2.07 REMARK 500 O HOH A 1006 O HOH A 1023 2.09 REMARK 500 O HOH A 1097 O HOH A 1098 2.10 REMARK 500 O HOH A 1048 O HOH A 1096 2.11 REMARK 500 OD1 ASN A 651 O HOH A 901 2.17 REMARK 500 OE1 GLU A 646 O HOH A 902 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 A1125 DISTANCE = 5.93 ANGSTROMS REMARK 525 HOH A1126 DISTANCE = 6.15 ANGSTROMS REMARK 525 HOH A1127 DISTANCE = 7.01 ANGSTROMS REMARK 525 HOH A1128 DISTANCE = 8.01 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue KGU A 801 DBREF 5MWZ A 626 740 UNP P55201 BRPF1_HUMAN 626 740 SEQADV 5MWZ 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 KGU A 801 33 HETNAM KGU ~{N}-[1,4-DIETHYL-2,3-BIS(OXIDANYLIDENE)-7-PIPERIDIN-1- HETNAM 2 KGU YL-QUINOXALIN-6-YL]-2-(4-METHYLPIPERAZIN-1-YL) HETNAM 3 KGU ETHANAMIDE FORMUL 2 KGU C24 H36 N6 O3 FORMUL 3 HOH *228(H2 O) HELIX 1 AA1 GLN A 629 ASP A 648 1 20 HELIX 2 AA2 PRO A 658 VAL A 662 5 5 HELIX 3 AA3 ASP A 664 ILE A 669 1 6 HELIX 4 AA4 ASP A 674 ALA A 684 1 11 HELIX 5 AA5 ASN A 689 ASN A 708 1 20 HELIX 6 AA6 THR A 712 LYS A 738 1 27 SITE 1 AC1 12 GLU A 627 ILE A 652 PHE A 653 VAL A 657 SITE 2 AC1 12 PRO A 658 TYR A 665 CYS A 704 TYR A 707 SITE 3 AC1 12 ASN A 708 PHE A 714 GLU A 737 HOH A 911 CRYST1 60.811 60.811 63.207 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 0.016444 0.009494 0.000000 0.00000 SCALE2 0.000000 0.018988 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015821 0.00000