HEADER TRANSCRIPTION 21-NOV-16 5MGE TITLE CRYSTAL STRUCTURE OF BAZ2B BROMODOMAIN IN COMPLEX WITH 1- TITLE 2 METHYLPYRIDINE DERIVATIVE 1 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 2054-2167; COMPND 5 SYNONYM: HWALP4; COMPND 6 ENGINEERED: YES; COMPND 7 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,D.SPILIOTOPOULOS,A.CAFLISCH REVDAT 3 17-JAN-24 5MGE 1 REMARK REVDAT 2 06-SEP-17 5MGE 1 JRNL REMARK REVDAT 1 12-APR-17 5MGE 0 JRNL AUTH D.SPILIOTOPOULOS,E.C.WAMHOFF,G.LOLLI,C.RADEMACHER,A.CAFLISCH JRNL TITL DISCOVERY OF BAZ2A BROMODOMAIN LIGANDS. JRNL REF EUR J MED CHEM V. 139 564 2017 JRNL REFN ISSN 1768-3254 JRNL PMID 28837921 JRNL DOI 10.1016/J.EJMECH.2017.08.028 REMARK 2 REMARK 2 RESOLUTION. 1.95 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.38 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 16672 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 849 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 48.3914 - 3.5431 1.00 2763 150 0.1486 0.1750 REMARK 3 2 3.5431 - 2.8123 1.00 2656 145 0.1900 0.2481 REMARK 3 3 2.8123 - 2.4569 0.99 2642 128 0.2018 0.2287 REMARK 3 4 2.4569 - 2.2322 0.99 2611 123 0.2045 0.2539 REMARK 3 5 2.2322 - 2.0722 0.99 2595 143 0.2178 0.2586 REMARK 3 6 2.0722 - 1.9500 0.99 2556 160 0.2459 0.2564 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.740 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.14 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 : 0.006 982 REMARK 3 ANGLE : 0.996 1321 REMARK 3 CHIRALITY : 0.034 141 REMARK 3 PLANARITY : 0.003 167 REMARK 3 DIHEDRAL : 13.886 375 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1856 THROUGH 1868 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.4776 -35.1070 -9.8861 REMARK 3 T TENSOR REMARK 3 T11: 0.2957 T22: 0.5349 REMARK 3 T33: 0.4738 T12: -0.0094 REMARK 3 T13: 0.0183 T23: 0.0393 REMARK 3 L TENSOR REMARK 3 L11: 0.0060 L22: 0.0688 REMARK 3 L33: 0.0696 L12: 0.0173 REMARK 3 L13: -0.0009 L23: -0.0020 REMARK 3 S TENSOR REMARK 3 S11: -0.4597 S12: -0.4313 S13: -0.2437 REMARK 3 S21: -0.2299 S22: -0.0775 S23: 0.1473 REMARK 3 S31: -0.4887 S32: 0.2707 S33: -0.0207 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1869 THROUGH 1943 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.0081 -17.6433 -3.9150 REMARK 3 T TENSOR REMARK 3 T11: 0.2430 T22: 0.2418 REMARK 3 T33: 0.2520 T12: 0.0047 REMARK 3 T13: 0.0036 T23: -0.0063 REMARK 3 L TENSOR REMARK 3 L11: 1.2147 L22: 0.5528 REMARK 3 L33: 0.8382 L12: -0.7854 REMARK 3 L13: 0.4873 L23: -0.1370 REMARK 3 S TENSOR REMARK 3 S11: 0.0560 S12: 0.0115 S13: -0.0627 REMARK 3 S21: -0.0157 S22: -0.0173 S23: -0.0122 REMARK 3 S31: -0.3208 S32: 0.0748 S33: 0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1944 THROUGH 1971 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.0689 -20.1666 7.3598 REMARK 3 T TENSOR REMARK 3 T11: 0.4053 T22: 0.3384 REMARK 3 T33: 0.2658 T12: 0.0804 REMARK 3 T13: -0.0212 T23: 0.0368 REMARK 3 L TENSOR REMARK 3 L11: 0.1801 L22: 0.0351 REMARK 3 L33: 0.3296 L12: 0.0436 REMARK 3 L13: 0.0016 L23: -0.0915 REMARK 3 S TENSOR REMARK 3 S11: -0.2464 S12: -0.2566 S13: -0.1804 REMARK 3 S21: 0.6400 S22: 0.0760 S23: 0.1739 REMARK 3 S31: -0.1021 S32: 0.1207 S33: -0.0004 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 5MGE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-NOV-16. REMARK 100 THE DEPOSITION ID IS D_1200002431. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUL-16 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 0.3.11, XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16759 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 48.380 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 7.70 REMARK 200 R MERGE FOR SHELL (I) : 0.78500 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: 4IR5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG500MME (20%), PEG1000 (2%), PEG3350 REMARK 280 (2%), PEG20000 (10%), MPD (2%), PH 7.5, VAPOR DIFFUSION, SITTING REMARK 280 DROP, 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 28.99000 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 28.99000 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 39.97450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 48.37650 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 39.97450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 48.37650 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 28.99000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 39.97450 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 48.37650 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 28.99000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 39.97450 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 48.37650 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: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7840 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 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 7MX A 2001 DBREF 5MGE A 1858 1971 UNP Q9UIF8 BAZ2B_HUMAN 2054 2167 SEQADV 5MGE SER A 1856 UNP Q9UIF8 EXPRESSION TAG SEQADV 5MGE MET A 1857 UNP Q9UIF8 EXPRESSION TAG SEQRES 1 A 116 SER MET SER VAL LYS LYS PRO LYS ARG ASP ASP SER LYS SEQRES 2 A 116 ASP LEU ALA LEU CYS SER MET ILE LEU THR GLU MET GLU SEQRES 3 A 116 THR HIS GLU ASP ALA TRP PRO PHE LEU LEU PRO VAL ASN SEQRES 4 A 116 LEU LYS LEU VAL PRO GLY TYR LYS LYS VAL ILE LYS LYS SEQRES 5 A 116 PRO MET ASP PHE SER THR ILE ARG GLU LYS LEU SER SER SEQRES 6 A 116 GLY GLN TYR PRO ASN LEU GLU THR PHE ALA LEU ASP VAL SEQRES 7 A 116 ARG LEU VAL PHE ASP ASN CYS GLU THR PHE ASN GLU ASP SEQRES 8 A 116 ASP SER ASP ILE GLY ARG ALA GLY HIS ASN MET ARG LYS SEQRES 9 A 116 TYR PHE GLU LYS LYS TRP THR ASP THR PHE LYS VAL HET 7MX A2001 14 HETNAM 7MX ETHYL 4-CHLORANYL-1-METHYL-6-OXIDANYLIDENE-PYRIDINE-3- HETNAM 2 7MX CARBOXYLATE FORMUL 2 7MX C9 H10 CL N O3 FORMUL 3 HOH *104(H2 O) HELIX 1 AA1 LYS A 1868 THR A 1882 1 15 HELIX 2 AA2 HIS A 1883 LEU A 1890 5 8 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 7 PRO A1888 PHE A1889 VAL A1893 VAL A1898 SITE 2 AC1 7 ASN A1944 HOH A2102 HOH A2148 CRYST1 79.949 96.753 57.980 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 0.012508 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010336 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017247 0.00000