HEADER TRANSCRIPTION 08-JUN-16 5L8T TITLE CRYSTAL STRUCTURE OF BAZ2B BROMODOMAIN IN COMPLEX WITH 3-AMINO-2- TITLE 2 METHYLPYRIDINE DERIVATIVE 2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN ADJACENT TO ZINC FINGER DOMAIN PROTEIN 2B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: BROMODOMAIN (RESIDUES 1858-1971); COMPND 5 SYNONYM: HWALP4; 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: 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,J.-R.MARCHAND,A.CAFLISCH REVDAT 3 10-JAN-24 5L8T 1 REMARK REVDAT 2 21-DEC-16 5L8T 1 JRNL REVDAT 1 26-OCT-16 5L8T 0 JRNL AUTH J.R.MARCHAND,G.LOLLI,A.CAFLISCH JRNL TITL DERIVATIVES OF 3-AMINO-2-METHYLPYRIDINE AS BAZ2B BROMODOMAIN JRNL TITL 2 LIGANDS: IN SILICO DISCOVERY AND IN CRYSTALLO VALIDATION. JRNL REF J. MED. CHEM. V. 59 9919 2016 JRNL REFN ISSN 1520-4804 JRNL PMID 27731638 JRNL DOI 10.1021/ACS.JMEDCHEM.6B01258 REMARK 2 REMARK 2 RESOLUTION. 1.85 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.19 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 19288 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 : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 978 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 48.1900 - 3.5387 0.99 2746 158 0.1630 0.1727 REMARK 3 2 3.5387 - 2.8088 0.99 2659 131 0.1916 0.2105 REMARK 3 3 2.8088 - 2.4538 0.97 2580 137 0.1909 0.2493 REMARK 3 4 2.4538 - 2.2294 0.99 2596 136 0.1971 0.2290 REMARK 3 5 2.2294 - 2.0696 0.99 2622 114 0.2111 0.2236 REMARK 3 6 2.0696 - 1.9476 0.99 2589 146 0.2419 0.3051 REMARK 3 7 1.9476 - 1.8501 0.98 2518 156 0.2984 0.3393 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.930 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.25 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 1004 REMARK 3 ANGLE : 1.069 1356 REMARK 3 CHIRALITY : 0.038 145 REMARK 3 PLANARITY : 0.004 171 REMARK 3 DIHEDRAL : 17.272 395 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): 1.4615 -34.6835 -9.9373 REMARK 3 T TENSOR REMARK 3 T11: 0.3766 T22: 0.4840 REMARK 3 T33: 0.5168 T12: 0.0055 REMARK 3 T13: 0.0734 T23: 0.1055 REMARK 3 L TENSOR REMARK 3 L11: 5.5114 L22: 0.0661 REMARK 3 L33: 0.6410 L12: 0.5414 REMARK 3 L13: -1.8756 L23: -0.1702 REMARK 3 S TENSOR REMARK 3 S11: -0.4007 S12: -0.6364 S13: -0.8768 REMARK 3 S21: -0.0140 S22: 0.0593 S23: 0.1153 REMARK 3 S31: -0.1021 S32: 0.3184 S33: 0.3337 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1869 THROUGH 1943 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.2162 -17.7437 -3.9330 REMARK 3 T TENSOR REMARK 3 T11: 0.3082 T22: 0.2350 REMARK 3 T33: 0.2291 T12: 0.0206 REMARK 3 T13: -0.0384 T23: 0.0125 REMARK 3 L TENSOR REMARK 3 L11: 2.7684 L22: 1.7741 REMARK 3 L33: 2.6819 L12: -0.2361 REMARK 3 L13: -0.6110 L23: 0.9675 REMARK 3 S TENSOR REMARK 3 S11: 0.0318 S12: 0.1137 S13: 0.0919 REMARK 3 S21: -0.1520 S22: -0.1010 S23: 0.0934 REMARK 3 S31: -0.3677 S32: -0.0620 S33: 0.0643 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1944 THROUGH 1971 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.5232 -19.9187 7.4053 REMARK 3 T TENSOR REMARK 3 T11: 0.3940 T22: 0.3214 REMARK 3 T33: 0.2130 T12: 0.0601 REMARK 3 T13: -0.0671 T23: 0.0394 REMARK 3 L TENSOR REMARK 3 L11: 3.2120 L22: 4.6811 REMARK 3 L33: 3.4873 L12: -0.8932 REMARK 3 L13: -0.5301 L23: 0.2904 REMARK 3 S TENSOR REMARK 3 S11: -0.3780 S12: -0.5378 S13: -0.0730 REMARK 3 S21: 0.7786 S22: 0.1603 S23: -0.1932 REMARK 3 S31: 0.0795 S32: 0.2742 S33: 0.0742 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 5L8T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1200000340. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAY-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) : 1.0 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 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19481 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 48.190 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.89 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.82400 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 (%): 70.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.15 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 28.83150 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 28.83150 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 40.41350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 48.19100 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 40.41350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 48.19100 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 28.83150 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 40.41350 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 48.19100 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 28.83150 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 40.41350 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 48.19100 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 6RR A 2001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5E9K RELATED DB: PDB REMARK 900 SAME PROTEIN IN COMPLEX WITH A SIMILAR HEAD GROUP DBREF 5L8T A 1858 1971 UNP Q9UIF8 BAZ2B_HUMAN 1858 1971 SEQADV 5L8T SER A 1856 UNP Q9UIF8 EXPRESSION TAG SEQADV 5L8T 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 6RR A2001 16 HETNAM 6RR ~{N}-[(3~{R})-1,1-BIS(OXIDANYLIDENE)THIAN-3-YL]-2- HETNAM 2 6RR METHYL-PYRIDIN-3-AMINE FORMUL 2 6RR C11 H16 N2 O2 S FORMUL 3 HOH *100(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 9 PRO A1888 VAL A1893 ASN A1894 LEU A1897 SITE 2 AC1 9 VAL A1898 TYR A1901 PHE A1943 ASN A1944 SITE 3 AC1 9 HOH A2115 CRYST1 80.827 96.382 57.663 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 0.012372 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010375 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017342 0.00000