HEADER TRANSCRIPTION 15-AUG-17 5ORB TITLE CRYSTAL STRUCTURE OF BAZ2B BROMODOMAIN IN COMPLEX WITH 1-METHYL- TITLE 2 CYCLOPENTAPYRAZOLE COMPOUND 30 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 1858-1972; 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.DALLE VEDOVE,J.-R.MARCHAND,A.CAFLISCH REVDAT 3 17-JAN-24 5ORB 1 REMARK REVDAT 2 01-NOV-17 5ORB 1 JRNL REVDAT 1 13-SEP-17 5ORB 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. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.39 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 72.0 REMARK 3 NUMBER OF REFLECTIONS : 9759 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) : 0.188 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.270 REMARK 3 FREE R VALUE TEST SET COUNT : 514 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 48.4068 - 3.3383 1.00 3301 194 0.1798 0.1927 REMARK 3 2 3.3383 - 2.6498 0.84 2706 142 0.2006 0.2690 REMARK 3 3 2.6498 - 2.3148 0.57 1806 95 0.2003 0.2490 REMARK 3 4 2.3148 - 2.1032 0.45 1432 83 0.1822 0.2373 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.810 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.99 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 1015 REMARK 3 ANGLE : 0.758 1367 REMARK 3 CHIRALITY : 0.043 144 REMARK 3 PLANARITY : 0.004 172 REMARK 3 DIHEDRAL : 16.492 629 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): 1.2830 -34.7727 -9.8650 REMARK 3 T TENSOR REMARK 3 T11: 0.1104 T22: 0.3716 REMARK 3 T33: 0.2668 T12: -0.0896 REMARK 3 T13: 0.0365 T23: 0.0804 REMARK 3 L TENSOR REMARK 3 L11: 0.0209 L22: 0.0272 REMARK 3 L33: 0.0143 L12: 0.0217 REMARK 3 L13: 0.0127 L23: 0.0363 REMARK 3 S TENSOR REMARK 3 S11: -0.0427 S12: 0.0182 S13: -0.1123 REMARK 3 S21: -0.1143 S22: 0.0437 S23: 0.2071 REMARK 3 S31: -0.0874 S32: 0.1123 S33: 0.0151 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1869 THROUGH 1882 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.4635 -29.8752 -2.0899 REMARK 3 T TENSOR REMARK 3 T11: 0.0832 T22: 0.0963 REMARK 3 T33: 0.2019 T12: -0.0228 REMARK 3 T13: -0.0470 T23: -0.0174 REMARK 3 L TENSOR REMARK 3 L11: 0.0145 L22: -0.0020 REMARK 3 L33: 0.0218 L12: -0.0019 REMARK 3 L13: 0.0169 L23: -0.0038 REMARK 3 S TENSOR REMARK 3 S11: -0.0124 S12: 0.0279 S13: -0.0316 REMARK 3 S21: -0.0333 S22: -0.0746 S23: 0.0545 REMARK 3 S31: 0.1003 S32: -0.0834 S33: -0.0464 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1883 THROUGH 1943 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.3863 -14.9387 -4.4675 REMARK 3 T TENSOR REMARK 3 T11: 0.1665 T22: 0.1238 REMARK 3 T33: 0.1116 T12: -0.0057 REMARK 3 T13: -0.0080 T23: -0.0083 REMARK 3 L TENSOR REMARK 3 L11: 0.1986 L22: 0.0677 REMARK 3 L33: 0.3486 L12: -0.0077 REMARK 3 L13: -0.0832 L23: -0.0347 REMARK 3 S TENSOR REMARK 3 S11: 0.1606 S12: 0.0514 S13: 0.0150 REMARK 3 S21: -0.0507 S22: -0.1023 S23: -0.0526 REMARK 3 S31: -0.3892 S32: 0.1107 S33: 0.0394 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1944 THROUGH 1971 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.6618 -19.8591 7.4849 REMARK 3 T TENSOR REMARK 3 T11: 0.2254 T22: 0.0791 REMARK 3 T33: 0.0979 T12: 0.1041 REMARK 3 T13: -0.0496 T23: 0.0437 REMARK 3 L TENSOR REMARK 3 L11: 0.0183 L22: 0.0065 REMARK 3 L33: 0.0853 L12: 0.0100 REMARK 3 L13: 0.0210 L23: -0.0033 REMARK 3 S TENSOR REMARK 3 S11: -0.0013 S12: -0.1566 S13: -0.0081 REMARK 3 S21: 0.1813 S22: -0.0504 S23: -0.0216 REMARK 3 S31: -0.0967 S32: 0.2065 S33: -0.0330 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DATA WERE STRONGLY ANISOTROPIC. DATA REMARK 3 WERE SUBJECTED TO ELLIPSOIDAL PROCESSING THROUGH THE STARANISO REMARK 3 SERVER (HTTP://STARANISO.GLOBALPHASING.ORG/CGI-BIN/STARANISO.CGI) REMARK 3 . AS SUCH, SPHERICAL COMPLETENESS IS LOW OVERALL AND IN HIGHEST REMARK 3 RESOLUTION SHELLS. INCLUDED DATA CONTRIBUTE HOWEVER RELEVANTLY REMARK 3 TO THE DENSITY MAPS. REMARK 4 REMARK 4 5ORB 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_1200006206. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JUN-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 : 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) : 1.00 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 : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9775 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.103 REMARK 200 RESOLUTION RANGE LOW (A) : 48.394 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 72.1 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 6.63 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 48.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 0.06000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 26.10 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 (%): 70.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.18 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 28.91000 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 28.91000 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 40.45300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 48.39400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 40.45300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 48.39400 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 28.91000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 40.45300 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 48.39400 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 28.91000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 40.45300 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 48.39400 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: 190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 3.0 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 JR6 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 DOMAIN BAZ2A COMPLEXED WITH A SIMILAR REMARK 900 COMPOUND REMARK 900 RELATED ID: 5OR9 RELATED DB: PDB REMARK 900 5OR9 CONTAINS THE SAME PROTEIN COMPLEXED WITH A SIMILAR COMPOUND DBREF 5ORB A 1858 1972 UNP Q9UIF8 BAZ2B_HUMAN 1858 1972 SEQADV 5ORB SER A 1856 UNP Q9UIF8 EXPRESSION TAG SEQADV 5ORB 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 JR6 A2001 22 HET EDO A2002 4 HETNAM JR6 2-(4-METHOXYPHENYL)SULFANYL-~{N}-(2-METHYL-5,6-DIHYDRO- HETNAM 2 JR6 4~{H}-CYCLOPENTA[C]PYRAZOL-3-YL)ETHANAMIDE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 JR6 C16 H19 N3 O2 S FORMUL 3 EDO C2 H6 O2 FORMUL 4 HOH *99(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 6 PRO A1888 VAL A1893 PHE A1943 ASN A1944 SITE 2 AC1 6 HOH A2116 HOH A2117 SITE 1 AC2 2 LYS A1907 HOH A2166 CRYST1 80.906 96.788 57.820 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 0.012360 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010332 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017295 0.00000