HEADER TRANSCRIPTION 15-OCT-15 5E9K TITLE CRYSTAL STRUCTURE OF BAZ2B BROMODOMAIN IN COMPLEX WITH FRAGMENT F275 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; 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,A.CAFLISCH REVDAT 3 10-JAN-24 5E9K 1 REMARK REVDAT 2 30-MAR-16 5E9K 1 JRNL REVDAT 1 16-MAR-16 5E9K 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. 2.07 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) : 2.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.09 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.320 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 14219 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1342 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 48.0900 - 4.4512 1.00 2553 136 0.1477 0.1609 REMARK 3 2 4.4512 - 3.5334 1.00 2543 137 0.1646 0.1887 REMARK 3 3 3.5334 - 3.0868 1.00 2548 139 0.2158 0.2512 REMARK 3 4 3.0868 - 2.8046 1.00 2552 132 0.2101 0.2616 REMARK 3 5 2.8046 - 2.6036 1.00 2534 136 0.2082 0.1932 REMARK 3 6 2.6036 - 2.4501 1.00 2556 139 0.2252 0.2730 REMARK 3 7 2.4501 - 2.3274 1.00 2517 133 0.2280 0.2603 REMARK 3 8 2.3274 - 2.2261 0.99 2522 131 0.2506 0.2672 REMARK 3 9 2.2261 - 2.1404 0.99 2514 131 0.2630 0.2760 REMARK 3 10 2.1404 - 2.0665 0.94 2441 128 0.2887 0.3272 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) : 29.280 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.71 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.55 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 : 0.007 981 REMARK 3 ANGLE : 1.077 1320 REMARK 3 CHIRALITY : 0.038 142 REMARK 3 PLANARITY : 0.004 168 REMARK 3 DIHEDRAL : 13.490 378 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): -1.3527 34.3013 -9.6453 REMARK 3 T TENSOR REMARK 3 T11: 0.3926 T22: 0.6332 REMARK 3 T33: 0.5843 T12: -0.0297 REMARK 3 T13: -0.0035 T23: -0.0495 REMARK 3 L TENSOR REMARK 3 L11: 2.8384 L22: -0.0054 REMARK 3 L33: -0.0253 L12: -0.1690 REMARK 3 L13: 0.2160 L23: -0.1102 REMARK 3 S TENSOR REMARK 3 S11: -0.5178 S12: -0.6975 S13: 0.5328 REMARK 3 S21: 0.0505 S22: 0.0002 S23: -0.0393 REMARK 3 S31: 0.3203 S32: -0.1956 S33: 0.5189 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1869 THROUGH 1882 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.4820 29.4867 -2.2624 REMARK 3 T TENSOR REMARK 3 T11: 0.2980 T22: 0.3179 REMARK 3 T33: 0.3864 T12: -0.0057 REMARK 3 T13: 0.0498 T23: -0.0044 REMARK 3 L TENSOR REMARK 3 L11: 6.5310 L22: 3.1929 REMARK 3 L33: 4.6301 L12: -3.2335 REMARK 3 L13: 3.9253 L23: -2.2870 REMARK 3 S TENSOR REMARK 3 S11: -0.1285 S12: 0.1267 S13: 0.2597 REMARK 3 S21: 0.2836 S22: -0.0018 S23: -0.2237 REMARK 3 S31: -0.2888 S32: 0.2355 S33: 0.1031 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1883 THROUGH 1943 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.6303 14.9628 -4.3879 REMARK 3 T TENSOR REMARK 3 T11: 0.3575 T22: 0.3210 REMARK 3 T33: 0.3292 T12: 0.0232 REMARK 3 T13: 0.0180 T23: -0.0044 REMARK 3 L TENSOR REMARK 3 L11: 2.5508 L22: 2.4692 REMARK 3 L33: 2.8669 L12: -0.0771 REMARK 3 L13: 0.1759 L23: 0.2630 REMARK 3 S TENSOR REMARK 3 S11: 0.0861 S12: 0.1072 S13: -0.1072 REMARK 3 S21: -0.0583 S22: -0.0590 S23: -0.1272 REMARK 3 S31: 0.4897 S32: -0.0362 S33: -0.0572 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1944 THROUGH 1971 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.7381 19.6643 7.3286 REMARK 3 T TENSOR REMARK 3 T11: 0.4259 T22: 0.4366 REMARK 3 T33: 0.3162 T12: 0.0774 REMARK 3 T13: 0.0477 T23: -0.0269 REMARK 3 L TENSOR REMARK 3 L11: 2.8462 L22: 4.2970 REMARK 3 L33: 2.7307 L12: -0.5649 REMARK 3 L13: 0.1354 L23: -0.1247 REMARK 3 S TENSOR REMARK 3 S11: -0.3736 S12: -0.5530 S13: 0.0992 REMARK 3 S21: 0.9715 S22: 0.2648 S23: 0.1632 REMARK 3 S31: 0.0756 S32: -0.3058 S33: 0.0267 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 5E9K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-OCT-15. REMARK 100 THE DEPOSITION ID IS D_1000214568. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUL-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 : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 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 : SCALA 3.3.22 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14219 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.067 REMARK 200 RESOLUTION RANGE LOW (A) : 48.090 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 8.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04800 REMARK 200 FOR THE DATA SET : 26.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8 REMARK 200 DATA REDUNDANCY IN SHELL : 8.50 REMARK 200 R MERGE FOR SHELL (I) : 0.39600 REMARK 200 R SYM FOR SHELL (I) : 0.39600 REMARK 200 FOR SHELL : 1.900 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 (%): 70.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.18 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 28.89700 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 28.89700 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 40.66550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 48.09050 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 40.66550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 48.09050 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 28.89700 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 40.66550 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 48.09050 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 28.89700 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 40.66550 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 48.09050 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: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7870 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 5KX A 2001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5DYU RELATED DB: PDB REMARK 900 5DYU CONTAINS THE SAME PROTEIN COMPLEXED WITH A DIFFERENT FRAGMENT REMARK 900 RELATED ID: 5DYX RELATED DB: PDB REMARK 900 5DYX CONTAINS THE SAME PROTEIN COMPLEXED WITH A DIFFERENT FRAGMENT REMARK 900 RELATED ID: 5E9I RELATED DB: PDB REMARK 900 5E9I CONTAINS THE SAME PROTEIN COMPLEXED WITH A DIFFERENT FRAGMENT DBREF 5E9K A 1858 1971 UNP Q9UIF8 BAZ2B_HUMAN 1954 2067 SEQADV 5E9K SER A 1856 UNP Q9UIF8 EXPRESSION TAG SEQADV 5E9K 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 5KX A2001 6 HETNAM 5KX 2-CHLORO-1H-IMIDAZOLE FORMUL 2 5KX C3 H3 CL N2 FORMUL 3 HOH *65(H2 O) HELIX 1 AA1 LYS A 1868 HIS A 1883 1 16 HELIX 2 AA2 GLU A 1884 TRP A 1887 5 4 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 A2129 HOH A2142 CRYST1 81.331 96.181 57.794 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 0.012295 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010397 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017303 0.00000