HEADER TRANSCRIPTION 25-SEP-15 5DYX TITLE CRYSTAL STRUCTURE OF BAZ2B BROMODOMAIN IN COMPLEX WITH FRAGMENT F59 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN ADJACENT TO ZINC FINGER DOMAIN PROTEIN 2B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: BROMODOMAIN (RESIDUES 2054-2168); 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,A.CAFLISCH REVDAT 3 10-JAN-24 5DYX 1 REMARK REVDAT 2 30-MAR-16 5DYX 1 JRNL REVDAT 1 16-MAR-16 5DYX 0 JRNL AUTH G.LOLLI,A.CAFLISCH JRNL TITL HIGH-THROUGHPUT FRAGMENT DOCKING INTO THE BAZ2B BROMODOMAIN: JRNL TITL 2 EFFICIENT IN SILICO SCREENING FOR X-RAY CRYSTALLOGRAPHY. JRNL REF ACS CHEM.BIOL. V. 11 800 2016 JRNL REFN ESSN 1554-8937 JRNL PMID 26942307 JRNL DOI 10.1021/ACSCHEMBIO.5B00914 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 19608 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 990 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 42.2800 - 3.5384 1.00 2778 157 0.1501 0.1659 REMARK 3 2 3.5384 - 2.8087 1.00 2695 133 0.1875 0.2165 REMARK 3 3 2.8087 - 2.4537 1.00 2659 144 0.1849 0.2351 REMARK 3 4 2.4537 - 2.2294 1.00 2641 135 0.1877 0.2283 REMARK 3 5 2.2294 - 2.0696 1.00 2652 117 0.1919 0.1987 REMARK 3 6 2.0696 - 1.9476 1.00 2620 148 0.2153 0.2543 REMARK 3 7 1.9476 - 1.8500 0.99 2573 156 0.2686 0.3031 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.650 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.02 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 : 0.007 979 REMARK 3 ANGLE : 1.000 1317 REMARK 3 CHIRALITY : 0.036 141 REMARK 3 PLANARITY : 0.004 166 REMARK 3 DIHEDRAL : 14.210 373 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1856 THROUGH 1868 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.4525 -34.4542 -9.8532 REMARK 3 T TENSOR REMARK 3 T11: 0.3324 T22: 0.5689 REMARK 3 T33: 0.5535 T12: -0.0128 REMARK 3 T13: -0.0192 T23: 0.0639 REMARK 3 L TENSOR REMARK 3 L11: 0.1054 L22: 0.3557 REMARK 3 L33: 0.0559 L12: -0.2322 REMARK 3 L13: -0.2386 L23: 0.3594 REMARK 3 S TENSOR REMARK 3 S11: -0.6622 S12: -0.6861 S13: -0.3645 REMARK 3 S21: -0.3334 S22: -0.0411 S23: 0.2459 REMARK 3 S31: -0.2530 S32: 0.4186 S33: -0.0105 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1869 THROUGH 1882 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.4322 -29.4155 -2.3438 REMARK 3 T TENSOR REMARK 3 T11: 0.3379 T22: 0.3054 REMARK 3 T33: 0.4871 T12: 0.0363 REMARK 3 T13: -0.0181 T23: 0.0062 REMARK 3 L TENSOR REMARK 3 L11: 0.1254 L22: 0.0912 REMARK 3 L33: 0.0350 L12: -0.0588 REMARK 3 L13: 0.0645 L23: -0.0249 REMARK 3 S TENSOR REMARK 3 S11: -0.2434 S12: 0.1833 S13: -0.8547 REMARK 3 S21: 0.3201 S22: 0.0591 S23: 0.4712 REMARK 3 S31: 0.6401 S32: -0.1787 S33: -0.0004 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1883 THROUGH 1910 ) REMARK 3 ORIGIN FOR THE GROUP (A): -25.0915 -10.0669 -3.1089 REMARK 3 T TENSOR REMARK 3 T11: 0.3434 T22: 0.2656 REMARK 3 T33: 0.3370 T12: 0.0537 REMARK 3 T13: 0.0321 T23: 0.0039 REMARK 3 L TENSOR REMARK 3 L11: 0.7700 L22: 0.5246 REMARK 3 L33: 0.3746 L12: -0.3800 REMARK 3 L13: 0.3922 L23: 0.3070 REMARK 3 S TENSOR REMARK 3 S11: -0.0802 S12: -0.1588 S13: 0.2823 REMARK 3 S21: -0.0859 S22: 0.0733 S23: 0.1804 REMARK 3 S31: -0.2522 S32: 0.0113 S33: 0.0002 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1911 THROUGH 1943 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.7470 -19.0945 -5.5610 REMARK 3 T TENSOR REMARK 3 T11: 0.2708 T22: 0.3000 REMARK 3 T33: 0.2500 T12: 0.0287 REMARK 3 T13: -0.0282 T23: -0.0202 REMARK 3 L TENSOR REMARK 3 L11: 1.0787 L22: 0.6904 REMARK 3 L33: 0.3824 L12: -0.6000 REMARK 3 L13: 0.2573 L23: -0.2404 REMARK 3 S TENSOR REMARK 3 S11: 0.1465 S12: 0.1842 S13: 0.0540 REMARK 3 S21: -0.1165 S22: -0.1494 S23: 0.0349 REMARK 3 S31: -0.1564 S32: 0.1876 S33: 0.0000 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1944 THROUGH 1971 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.6948 -20.0885 7.2337 REMARK 3 T TENSOR REMARK 3 T11: 0.4477 T22: 0.3764 REMARK 3 T33: 0.2741 T12: 0.1295 REMARK 3 T13: -0.0018 T23: 0.0256 REMARK 3 L TENSOR REMARK 3 L11: 0.1582 L22: 0.2418 REMARK 3 L33: 0.8124 L12: 0.1185 REMARK 3 L13: 0.2194 L23: -0.1059 REMARK 3 S TENSOR REMARK 3 S11: -0.5346 S12: -0.6287 S13: -0.1259 REMARK 3 S21: 1.0210 S22: 0.4131 S23: -0.0141 REMARK 3 S31: -0.0270 S32: 0.2995 S33: -0.0009 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 5DYX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-SEP-15. REMARK 100 THE DEPOSITION ID IS D_1000214054. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-MAY-15 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) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19634 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 48.120 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.8000 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 (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.30 REMARK 200 R MERGE FOR SHELL (I) : 0.73300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 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 (%): 70.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.17 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 28.89150 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 28.89150 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 40.56450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 48.11800 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 40.56450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 48.11800 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 28.89150 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 40.56450 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 48.11800 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 28.89150 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 40.56450 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 48.11800 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7850 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 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ADE A 2001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5DYU RELATED DB: PDB DBREF 5DYX A 1858 1971 UNP Q9UIF8 BAZ2B_HUMAN 1954 2067 SEQADV 5DYX SER A 1856 UNP Q9UIF8 EXPRESSION TAG SEQADV 5DYX 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 ADE A2001 10 HETNAM ADE ADENINE FORMUL 2 ADE C5 H5 N5 FORMUL 3 HOH *127(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 PHE A1943 ASN A1944 HOH A2107 SITE 2 AC1 6 HOH A2109 HOH A2110 CRYST1 81.129 96.236 57.783 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 0.012326 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010391 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017306 0.00000