HEADER DNA BINDING PROTEIN 30-MAY-17 5O4S TITLE CRYSTAL STRUCTURE OF THE HUMAN BRPF1 BROMODOMAIN IN COMPLEX WITH BZ135 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEREGRIN; COMPND 3 CHAIN: A, B; 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 17-JAN-24 5O4S 1 REMARK REVDAT 2 27-JUN-18 5O4S 1 JRNL REVDAT 1 13-JUN-18 5O4S 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. 1.75 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 29017 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.910 REMARK 3 FREE R VALUE TEST SET COUNT : 2004 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 38.0134 - 4.2160 1.00 1991 142 0.1688 0.1953 REMARK 3 2 4.2160 - 3.3470 1.00 1956 151 0.1549 0.1920 REMARK 3 3 3.3470 - 2.9241 1.00 1917 143 0.1817 0.2397 REMARK 3 4 2.9241 - 2.6568 1.00 1948 147 0.1957 0.2512 REMARK 3 5 2.6568 - 2.4664 1.00 1922 143 0.1979 0.2481 REMARK 3 6 2.4664 - 2.3210 1.00 1914 143 0.1913 0.2157 REMARK 3 7 2.3210 - 2.2048 1.00 1937 145 0.1781 0.2330 REMARK 3 8 2.2048 - 2.1088 1.00 1931 143 0.1727 0.2029 REMARK 3 9 2.1088 - 2.0277 1.00 1903 135 0.1699 0.2300 REMARK 3 10 2.0277 - 1.9577 1.00 1931 140 0.1744 0.2709 REMARK 3 11 1.9577 - 1.8965 1.00 1932 143 0.2121 0.2543 REMARK 3 12 1.8965 - 1.8423 1.00 1903 147 0.2228 0.3016 REMARK 3 13 1.8423 - 1.7938 1.00 1936 141 0.2291 0.3299 REMARK 3 14 1.7938 - 1.7500 0.99 1892 141 0.2545 0.2977 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.360 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 : 0.006 1964 REMARK 3 ANGLE : 0.722 2663 REMARK 3 CHIRALITY : 0.044 280 REMARK 3 PLANARITY : 0.004 394 REMARK 3 DIHEDRAL : 18.751 1224 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): 2.0436 4.6943 8.7135 REMARK 3 T TENSOR REMARK 3 T11: 0.2399 T22: 0.2318 REMARK 3 T33: 0.2396 T12: -0.0182 REMARK 3 T13: -0.0090 T23: 0.0276 REMARK 3 L TENSOR REMARK 3 L11: 0.6721 L22: 0.8266 REMARK 3 L33: 0.8053 L12: -0.1478 REMARK 3 L13: -0.2445 L23: 0.1795 REMARK 3 S TENSOR REMARK 3 S11: -0.0175 S12: -0.0847 S13: 0.0036 REMARK 3 S21: 0.0641 S22: 0.0099 S23: -0.0230 REMARK 3 S31: 0.0399 S32: -0.0222 S33: 0.0000 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 5O4S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-MAY-17. REMARK 100 THE DEPOSITION ID IS D_1200005183. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-FEB-17 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) : 1.0000 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 : 29072 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 38.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 13.20 REMARK 200 R MERGE (I) : 0.15100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 12.90 REMARK 200 R MERGE FOR SHELL (I) : 0.73000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.100 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: 4LC2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 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 297K 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 31.34500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 SER A 625 REMARK 465 MET A 626 REMARK 465 GLU A 627 REMARK 465 GLY A 740 REMARK 465 SER B 625 REMARK 465 MET B 626 REMARK 465 GLU B 627 REMARK 465 MET B 628 REMARK 465 GLY B 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 MET A 628 CG SD CE REMARK 470 LYS A 670 CG CD CE NZ REMARK 470 LYS A 679 CE NZ REMARK 470 GLN A 731 CD OE1 NE2 REMARK 470 GLU A 737 CG CD OE1 OE2 REMARK 470 LYS B 670 CE NZ REMARK 470 GLN B 731 CD OE1 NE2 REMARK 470 GLU B 737 CG CD OE1 OE2 REMARK 470 LYS B 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 B 960 O HOH B 972 1.98 REMARK 500 O HOH B 969 O HOH B 985 2.16 REMARK 500 O HOH B 912 O HOH B 972 2.19 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 A1017 DISTANCE = 6.24 ANGSTROMS REMARK 525 HOH B1007 DISTANCE = 6.78 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9KW A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO3 A 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9KW B 801 DBREF 5O4S A 626 740 UNP P55201 BRPF1_HUMAN 626 740 DBREF 5O4S B 626 740 UNP P55201 BRPF1_HUMAN 626 740 SEQADV 5O4S SER A 625 UNP P55201 EXPRESSION TAG SEQADV 5O4S SER B 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 SEQRES 1 B 116 SER MET GLU MET GLN LEU THR PRO PHE LEU ILE LEU LEU SEQRES 2 B 116 ARG LYS THR LEU GLU GLN LEU GLN GLU LYS ASP THR GLY SEQRES 3 B 116 ASN ILE PHE SER GLU PRO VAL PRO LEU SER GLU VAL PRO SEQRES 4 B 116 ASP TYR LEU ASP HIS ILE LYS LYS PRO MET ASP PHE PHE SEQRES 5 B 116 THR MET LYS GLN ASN LEU GLU ALA TYR ARG TYR LEU ASN SEQRES 6 B 116 PHE ASP ASP PHE GLU GLU ASP PHE ASN LEU ILE VAL SER SEQRES 7 B 116 ASN CYS LEU LYS TYR ASN ALA LYS ASP THR ILE PHE TYR SEQRES 8 B 116 ARG ALA ALA VAL ARG LEU ARG GLU GLN GLY GLY ALA VAL SEQRES 9 B 116 LEU ARG GLN ALA ARG ARG GLN ALA GLU LYS MET GLY HET 9KW A 801 34 HET NO3 A 802 4 HET 9KW B 801 34 HETNAM 9KW ~{N}-[1,4-DIMETHYL-7-MORPHOLIN-4-YL-2,3- HETNAM 2 9KW BIS(OXIDANYLIDENE)QUINOXALIN-6-YL]-5,6,7,8- HETNAM 3 9KW TETRAHYDRONAPHTHALENE-2-SULFONAMIDE HETNAM NO3 NITRATE ION FORMUL 3 9KW 2(C24 H28 N4 O5 S) FORMUL 4 NO3 N O3 1- FORMUL 6 HOH *224(H2 O) HELIX 1 AA1 THR A 631 ASP A 648 1 18 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 LYS A 738 1 27 HELIX 6 AA6 THR B 631 LYS B 647 1 17 HELIX 7 AA7 ASP B 664 ILE B 669 1 6 HELIX 8 AA8 ASP B 674 ALA B 684 1 11 HELIX 9 AA9 ASN B 689 ASN B 708 1 20 HELIX 10 AB1 THR B 712 LYS B 738 1 27 SITE 1 AC1 12 ILE A 652 PHE A 653 PRO A 658 GLU A 661 SITE 2 AC1 12 VAL A 662 CYS A 704 TYR A 707 ASN A 708 SITE 3 AC1 12 PHE A 714 HOH A 915 HOH A 931 LYS B 639 SITE 1 AC2 6 GLU A 694 LEU A 729 ARG A 733 ASP B 691 SITE 2 AC2 6 ARG B 733 HOH B 918 SITE 1 AC3 11 LYS A 639 ILE B 652 PRO B 658 GLU B 661 SITE 2 AC3 11 VAL B 662 CYS B 704 TYR B 707 ASN B 708 SITE 3 AC3 11 PHE B 714 HOH B 911 HOH B 930 CRYST1 48.700 62.690 48.820 90.00 101.81 90.00 P 1 21 1 4 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 0.020534 0.000000 0.004293 0.00000 SCALE2 0.000000 0.015952 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020926 0.00000