HEADER TRANSCRIPTION 15-OCT-15 5E9L TITLE CRYSTAL STRUCTURE OF BAZ2B BROMODOMAIN IN COMPLEX WITH FRAGMENT F103 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 5E9L 1 REMARK REVDAT 2 30-MAR-16 5E9L 1 JRNL REVDAT 1 16-MAR-16 5E9L 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. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 17998 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.410 REMARK 3 FREE R VALUE TEST SET COUNT : 974 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 48.1000 - 3.6344 0.99 2564 134 0.1543 0.1729 REMARK 3 2 3.6344 - 2.8848 1.00 2454 146 0.1846 0.2221 REMARK 3 3 2.8848 - 2.5202 0.99 2399 147 0.1781 0.2117 REMARK 3 4 2.5202 - 2.2898 0.99 2428 144 0.1863 0.2772 REMARK 3 5 2.2898 - 2.1256 0.99 2374 153 0.1985 0.2313 REMARK 3 6 2.1256 - 2.0003 0.99 2411 130 0.2340 0.2287 REMARK 3 7 2.0003 - 1.9001 0.99 2394 120 0.2762 0.3483 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.78 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.21 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 : 0.007 998 REMARK 3 ANGLE : 1.036 1347 REMARK 3 CHIRALITY : 0.039 145 REMARK 3 PLANARITY : 0.004 170 REMARK 3 DIHEDRAL : 13.912 387 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): -1.1945 34.3308 -9.8557 REMARK 3 T TENSOR REMARK 3 T11: 0.3400 T22: 0.4249 REMARK 3 T33: 0.5084 T12: -0.0197 REMARK 3 T13: 0.0273 T23: -0.0753 REMARK 3 L TENSOR REMARK 3 L11: 0.0323 L22: 0.1572 REMARK 3 L33: 0.1284 L12: 0.0775 REMARK 3 L13: 0.0573 L23: -0.1885 REMARK 3 S TENSOR REMARK 3 S11: -0.3999 S12: -0.4490 S13: 0.1331 REMARK 3 S21: -0.1006 S22: -0.0891 S23: -0.2068 REMARK 3 S31: 0.4933 S32: -0.2355 S33: -0.0084 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1869 THROUGH 1943 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.4454 17.7766 -4.0270 REMARK 3 T TENSOR REMARK 3 T11: 0.2340 T22: 0.2382 REMARK 3 T33: 0.2462 T12: 0.0110 REMARK 3 T13: 0.0146 T23: 0.0037 REMARK 3 L TENSOR REMARK 3 L11: 1.7860 L22: 0.5330 REMARK 3 L33: 0.9463 L12: -0.6816 REMARK 3 L13: -0.0637 L23: -0.0999 REMARK 3 S TENSOR REMARK 3 S11: 0.0621 S12: 0.0794 S13: 0.0677 REMARK 3 S21: -0.0251 S22: -0.0212 S23: -0.0845 REMARK 3 S31: 0.1370 S32: -0.0617 S33: 0.0001 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1944 THROUGH 1971 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.8275 19.6972 7.3268 REMARK 3 T TENSOR REMARK 3 T11: 0.4265 T22: 0.3348 REMARK 3 T33: 0.2625 T12: 0.1109 REMARK 3 T13: 0.0301 T23: -0.0321 REMARK 3 L TENSOR REMARK 3 L11: 0.3386 L22: 0.2036 REMARK 3 L33: 0.4572 L12: 0.2967 REMARK 3 L13: 0.0278 L23: 0.1795 REMARK 3 S TENSOR REMARK 3 S11: -0.3863 S12: -0.5754 S13: 0.1659 REMARK 3 S21: 0.8022 S22: 0.2976 S23: -0.0518 REMARK 3 S31: 0.0504 S32: -0.3844 S33: 0.0002 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 5E9L 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_1000214571. 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 : AIMLESS 0.3.11 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18071 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 48.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 REMARK 200 R MERGE FOR SHELL (I) : 0.71500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 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 (%): 70.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.16 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 28.88950 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 28.88950 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 40.45950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 48.10450 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 40.45950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 48.10450 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 28.88950 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 40.45950 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 48.10450 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 28.88950 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 40.45950 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 48.10450 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: 7790 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 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2222 DISTANCE = 5.84 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 6AI 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 REMARK 900 RELATED ID: 5E9K RELATED DB: PDB REMARK 900 5E9K CONTAINS THE SAME PROTEIN COMPLEXED WITH A DIFFERENT FRAGMENT DBREF 5E9L A 1858 1971 UNP Q9UIF8 BAZ2B_HUMAN 1954 2067 SEQADV 5E9L SER A 1856 UNP Q9UIF8 EXPRESSION TAG SEQADV 5E9L 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 6AI A2001 10 HETNAM 6AI 1H-INDAZOL-6-AMINE FORMUL 2 6AI C7 H7 N3 FORMUL 3 HOH *122(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 PHE A 1969 1 22 SITE 1 AC1 3 ASN A1944 ILE A1950 HOH A2124 CRYST1 80.919 96.209 57.779 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 0.012358 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010394 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017307 0.00000