HEADER TRANSCRIPTION 15-AUG-17 5OR9 TITLE CRYSTAL STRUCTURE OF BAZ2B BROMODOMAIN IN COMPLEX WITH 1-METHYL- TITLE 2 CYCLOPENTAPYRAZOLE COMPOUND 13 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN ADJACENT TO ZINC FINGER DOMAIN PROTEIN 2B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: BROMODOMAIN, UNP RESIDUES 1954-2068; COMPND 5 SYNONYM: HWALP4; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 OTHER_DETAILS: FIRST TWO RESIDUES SM DERIVE FROM THE EXPRESSION TAG SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: BAZ2B, KIAA1476; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FOUR HELICAL BUNDLE, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR G.LOLLI,A.D.VEDOVE,J.-R.MARCHAND,A.CAFLISCH REVDAT 3 17-JAN-24 5OR9 1 REMARK REVDAT 2 01-NOV-17 5OR9 1 JRNL REVDAT 1 13-SEP-17 5OR9 0 JRNL AUTH J.R.MARCHAND,A.DALLE VEDOVE,G.LOLLI,A.CAFLISCH JRNL TITL DISCOVERY OF INHIBITORS OF FOUR BROMODOMAINS BY JRNL TITL 2 FRAGMENT-ANCHORED LIGAND DOCKING. JRNL REF J CHEM INF MODEL V. 57 2584 2017 JRNL REFN ESSN 1549-960X JRNL PMID 28862840 JRNL DOI 10.1021/ACS.JCIM.7B00336 REMARK 2 REMARK 2 RESOLUTION. 2.00 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.72 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 15606 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.180 REMARK 3 FREE R VALUE TEST SET COUNT : 808 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 40.7304 - 3.6336 1.00 2612 131 0.1665 0.1804 REMARK 3 2 3.6336 - 2.8843 1.00 2461 149 0.1885 0.2226 REMARK 3 3 2.8843 - 2.5198 1.00 2450 134 0.1782 0.1899 REMARK 3 4 2.5198 - 2.2894 0.99 2456 139 0.2020 0.2220 REMARK 3 5 2.2894 - 2.1254 0.98 2394 129 0.2311 0.2567 REMARK 3 6 2.1254 - 2.0001 0.98 2425 126 0.2730 0.2909 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 27.410 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 1014 REMARK 3 ANGLE : 0.800 1369 REMARK 3 CHIRALITY : 0.044 144 REMARK 3 PLANARITY : 0.004 171 REMARK 3 DIHEDRAL : 16.123 622 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1856 THROUGH 1868 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.4641 34.3934 -9.7388 REMARK 3 T TENSOR REMARK 3 T11: 0.3343 T22: 0.5552 REMARK 3 T33: 0.5146 T12: 0.0164 REMARK 3 T13: -0.0433 T23: -0.0331 REMARK 3 L TENSOR REMARK 3 L11: 0.0354 L22: -0.0022 REMARK 3 L33: -0.0348 L12: 0.0318 REMARK 3 L13: 0.0883 L23: -0.0943 REMARK 3 S TENSOR REMARK 3 S11: -0.2543 S12: -0.3333 S13: 0.2519 REMARK 3 S21: -0.1489 S22: 0.0264 S23: -0.1470 REMARK 3 S31: 0.2949 S32: -0.1700 S33: -0.0005 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1869 THROUGH 1882 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.4355 29.9085 -2.0626 REMARK 3 T TENSOR REMARK 3 T11: 0.2643 T22: 0.3375 REMARK 3 T33: 0.3893 T12: -0.0016 REMARK 3 T13: 0.0116 T23: -0.0187 REMARK 3 L TENSOR REMARK 3 L11: 0.0351 L22: 0.0053 REMARK 3 L33: -0.0060 L12: -0.0315 REMARK 3 L13: -0.0351 L23: -0.0287 REMARK 3 S TENSOR REMARK 3 S11: -0.1023 S12: 0.0913 S13: 0.1052 REMARK 3 S21: 0.0572 S22: -0.0379 S23: -0.1378 REMARK 3 S31: -0.2614 S32: 0.1410 S33: 0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1883 THROUGH 1943 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.3456 15.1946 -4.3357 REMARK 3 T TENSOR REMARK 3 T11: 0.3015 T22: 0.2644 REMARK 3 T33: 0.2853 T12: -0.0080 REMARK 3 T13: 0.0022 T23: 0.0015 REMARK 3 L TENSOR REMARK 3 L11: 0.7758 L22: 0.2535 REMARK 3 L33: 0.6815 L12: -0.2474 REMARK 3 L13: -0.2053 L23: 0.0576 REMARK 3 S TENSOR REMARK 3 S11: 0.0726 S12: 0.0699 S13: -0.0899 REMARK 3 S21: -0.1693 S22: -0.0814 S23: 0.0195 REMARK 3 S31: 0.3812 S32: -0.0185 S33: 0.0001 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1944 THROUGH 1971 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.6107 20.2646 7.2938 REMARK 3 T TENSOR REMARK 3 T11: 0.4964 T22: 0.3910 REMARK 3 T33: 0.3374 T12: 0.0675 REMARK 3 T13: 0.0302 T23: -0.0240 REMARK 3 L TENSOR REMARK 3 L11: 0.1014 L22: 0.0779 REMARK 3 L33: 0.5124 L12: 0.0181 REMARK 3 L13: -0.1542 L23: 0.0637 REMARK 3 S TENSOR REMARK 3 S11: -0.2152 S12: -0.3492 S13: 0.0521 REMARK 3 S21: 0.5119 S22: 0.1984 S23: 0.0050 REMARK 3 S31: -0.0723 S32: -0.2058 S33: 0.0001 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 5OR9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-AUG-17. REMARK 100 THE DEPOSITION ID IS D_1200006205. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUL-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 5.2R REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.32 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15678 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 48.320 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 7.50 REMARK 200 R MERGE FOR SHELL (I) : 0.66800 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: 5DYU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG500MME, 2% PEG1000, 2% PEG3350, REMARK 280 10% PEG20000, 2% MPD, PH 7.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 28.79200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 28.79200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 40.72200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 48.32300 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 40.72200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 48.32300 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 28.79200 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 40.72200 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 48.32300 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 28.79200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 40.72200 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 48.32300 REMARK 290 SMTRY3 8 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 2.0 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 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 1972 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue JR5 A 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 2002 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5OR8 RELATED DB: PDB REMARK 900 5OR8 CONTAINS THE SIMILAR BROMODOMAIN BAZ2A COMPLEXED WITH A REMARK 900 SIMILAR COMPOUND DBREF 5OR9 A 1858 1972 UNP Q9UIF8 BAZ2B_HUMAN 1954 2068 SEQADV 5OR9 SER A 1856 UNP Q9UIF8 EXPRESSION TAG SEQADV 5OR9 MET A 1857 UNP Q9UIF8 EXPRESSION TAG SEQRES 1 A 117 SER MET SER VAL LYS LYS PRO LYS ARG ASP ASP SER LYS SEQRES 2 A 117 ASP LEU ALA LEU CYS SER MET ILE LEU THR GLU MET GLU SEQRES 3 A 117 THR HIS GLU ASP ALA TRP PRO PHE LEU LEU PRO VAL ASN SEQRES 4 A 117 LEU LYS LEU VAL PRO GLY TYR LYS LYS VAL ILE LYS LYS SEQRES 5 A 117 PRO MET ASP PHE SER THR ILE ARG GLU LYS LEU SER SER SEQRES 6 A 117 GLY GLN TYR PRO ASN LEU GLU THR PHE ALA LEU ASP VAL SEQRES 7 A 117 ARG LEU VAL PHE ASP ASN CYS GLU THR PHE ASN GLU ASP SEQRES 8 A 117 ASP SER ASP ILE GLY ARG ALA GLY HIS ASN MET ARG LYS SEQRES 9 A 117 TYR PHE GLU LYS LYS TRP THR ASP THR PHE LYS VAL SER HET JR5 A2001 27 HET EDO A2002 4 HETNAM JR5 (2~{S})-1-(4-FLUOROPHENYL)SULFONYL-~{N}-(2-METHYL-5,6- HETNAM 2 JR5 DIHYDRO-4~{H}-CYCLOPENTA[C]PYRAZOL-3-YL)PYRROLIDINE-2- HETNAM 3 JR5 CARBOXAMIDE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 JR5 C18 H21 F N4 O3 S FORMUL 3 EDO C2 H6 O2 FORMUL 4 HOH *93(H2 O) HELIX 1 AA1 LYS A 1868 HIS A 1883 1 16 HELIX 2 AA2 GLU A 1884 LEU A 1890 5 7 HELIX 3 AA3 GLY A 1900 ILE A 1905 1 6 HELIX 4 AA4 ASP A 1910 SER A 1920 1 11 HELIX 5 AA5 ASN A 1925 ASN A 1944 1 20 HELIX 6 AA6 SER A 1948 LYS A 1970 1 23 SITE 1 AC1 12 LYS A1861 TRP A1887 PRO A1888 PHE A1889 SITE 2 AC1 12 LEU A1891 PRO A1892 VAL A1893 PHE A1943 SITE 3 AC1 12 ASN A1944 ILE A1950 HOH A2110 HOH A2138 SITE 1 AC2 1 LYS A1896 CRYST1 81.444 96.646 57.584 90.00 90.00 90.00 C 2 2 21 8 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 0.012278 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010347 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017366 0.00000