HEADER TRANSCRIPTION 10-JAN-18 6FGH TITLE CRYSTAL STRUCTURE OF BAZ2A BROMODOMAIN IN COMPLEX WITH 3-AMINO-2- TITLE 2 METHYLPYRIDINE DERIVATIVE 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN ADJACENT TO ZINC FINGER DOMAIN PROTEIN 2A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: BROMODOMAIN (RESIDUES 1796-1899); COMPND 5 SYNONYM: TRANSCRIPTION TERMINATION FACTOR I-INTERACTING PROTEIN 5, COMPND 6 TIP5,HWALP3; COMPND 7 ENGINEERED: YES; COMPND 8 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: BAZ2A, KIAA0314, TIP5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FOUR HELICAL BUNDLE, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR A.DALLE VEDOVE,J.-R.MARCHAND,G.LOLLI,A.CAFLISCH REVDAT 3 17-JAN-24 6FGH 1 REMARK REVDAT 2 29-AUG-18 6FGH 1 JRNL REVDAT 1 30-MAY-18 6FGH 0 JRNL AUTH A.DALLE VEDOVE,D.SPILIOTOPOULOS,V.G.D'AGOSTINO,J.R.MARCHAND, JRNL AUTH 2 A.UNZUE,C.NEVADO,G.LOLLI,A.CAFLISCH JRNL TITL STRUCTURAL ANALYSIS OF SMALL-MOLECULE BINDING TO THE BAZ2A JRNL TITL 2 AND BAZ2B BROMODOMAINS. JRNL REF CHEMMEDCHEM V. 13 1479 2018 JRNL REFN ESSN 1860-7187 JRNL PMID 29770599 JRNL DOI 10.1002/CMDC.201800234 REMARK 2 REMARK 2 RESOLUTION. 2.10 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.26 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 10258 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.450 REMARK 3 FREE R VALUE TEST SET COUNT : 559 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 41.2645 - 3.3332 1.00 2474 163 0.1616 0.1904 REMARK 3 2 3.3332 - 2.6458 1.00 2415 137 0.1936 0.2204 REMARK 3 3 2.6458 - 2.3114 1.00 2424 133 0.2127 0.2388 REMARK 3 4 2.3114 - 2.1000 0.99 2386 126 0.2753 0.3208 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.060 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.26 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 : 0.006 905 REMARK 3 ANGLE : 0.780 1221 REMARK 3 CHIRALITY : 0.045 121 REMARK 3 PLANARITY : 0.005 158 REMARK 3 DIHEDRAL : 6.270 528 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 1796 THROUGH 1810 ) REMARK 3 ORIGIN FOR THE GROUP (A): -33.0148 20.1908 -9.1219 REMARK 3 T TENSOR REMARK 3 T11: 0.2524 T22: 0.2842 REMARK 3 T33: 0.3502 T12: -0.1584 REMARK 3 T13: 0.0256 T23: -0.0079 REMARK 3 L TENSOR REMARK 3 L11: 0.3139 L22: 0.0166 REMARK 3 L33: 0.2589 L12: -0.0472 REMARK 3 L13: 0.0709 L23: 0.0374 REMARK 3 S TENSOR REMARK 3 S11: 0.0355 S12: -0.1237 S13: -0.1755 REMARK 3 S21: 0.1504 S22: -0.1274 S23: -0.1370 REMARK 3 S31: 0.2443 S32: -0.2433 S33: -0.0403 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1811 THROUGH 1829 ) REMARK 3 ORIGIN FOR THE GROUP (A): -38.3013 36.8256 -19.8772 REMARK 3 T TENSOR REMARK 3 T11: 0.1498 T22: 0.5788 REMARK 3 T33: 0.2177 T12: -0.0147 REMARK 3 T13: 0.0010 T23: -0.0507 REMARK 3 L TENSOR REMARK 3 L11: 0.0049 L22: 0.6226 REMARK 3 L33: 1.0647 L12: 0.0135 REMARK 3 L13: -0.0581 L23: -0.6245 REMARK 3 S TENSOR REMARK 3 S11: -0.0289 S12: 0.0689 S13: -0.0259 REMARK 3 S21: -0.0971 S22: -0.0572 S23: 0.0153 REMARK 3 S31: 0.1362 S32: -0.3307 S33: -0.0282 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1830 THROUGH 1872 ) REMARK 3 ORIGIN FOR THE GROUP (A): -29.8256 28.1931 -21.1449 REMARK 3 T TENSOR REMARK 3 T11: 0.1848 T22: 0.3188 REMARK 3 T33: 0.2341 T12: -0.1219 REMARK 3 T13: 0.0605 T23: -0.0993 REMARK 3 L TENSOR REMARK 3 L11: 0.1165 L22: 0.2439 REMARK 3 L33: 0.5856 L12: 0.0454 REMARK 3 L13: 0.0764 L23: -0.2009 REMARK 3 S TENSOR REMARK 3 S11: -0.2130 S12: 0.3332 S13: -0.1933 REMARK 3 S21: -0.1258 S22: 0.0695 S23: -0.1760 REMARK 3 S31: 0.0787 S32: -0.1244 S33: -0.0524 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1873 THROUGH 1898 ) REMARK 3 ORIGIN FOR THE GROUP (A): -27.8195 34.7017 -9.3747 REMARK 3 T TENSOR REMARK 3 T11: 0.1143 T22: 0.2726 REMARK 3 T33: 0.2206 T12: -0.0809 REMARK 3 T13: -0.0405 T23: 0.0135 REMARK 3 L TENSOR REMARK 3 L11: 0.1396 L22: 0.0826 REMARK 3 L33: 1.6961 L12: -0.0566 REMARK 3 L13: -0.4470 L23: 0.0578 REMARK 3 S TENSOR REMARK 3 S11: 0.0995 S12: -0.0210 S13: -0.1431 REMARK 3 S21: 0.1266 S22: -0.0501 S23: -0.0044 REMARK 3 S31: -0.1430 S32: -0.1806 S33: 0.0603 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 6FGH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-JAN-18. REMARK 100 THE DEPOSITION ID IS D_1200008267. 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) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.3.11 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10275 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 47.640 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.800 REMARK 200 R MERGE (I) : 0.14600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.40 REMARK 200 R MERGE FOR SHELL (I) : 1.20800 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: 5MGJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3350, 0.2 M MGCL2, PH 7.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 11.01333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 22.02667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 22.02667 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 11.01333 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: 6300 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2044 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1794 REMARK 465 SER A 1795 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 6RZ A 1901 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5L96 RELATED DB: PDB REMARK 900 5L96 CONTAINS THE SAME SMALL MOLECULE COMPLEXED WITH THE PARALOG REMARK 900 BROMODOMAIN BAZ2B REMARK 900 RELATED ID: 5L8T RELATED DB: PDB REMARK 900 5L8T CONTAINS A SIMILAR SMALL MOLECULE COMPLEXED WITH THE PARALOG REMARK 900 BROMODOMAIN BAZ2B DBREF 6FGH A 1796 1898 UNP Q9UIF9 BAZ2A_HUMAN 1796 1898 SEQADV 6FGH MET A 1794 UNP Q9UIF9 INITIATING METHIONINE SEQADV 6FGH SER A 1795 UNP Q9UIF9 EXPRESSION TAG SEQRES 1 A 105 MET SER HIS SER ASP LEU THR PHE CYS GLU ILE ILE LEU SEQRES 2 A 105 MET GLU MET GLU SER HIS ASP ALA ALA TRP PRO PHE LEU SEQRES 3 A 105 GLU PRO VAL ASN PRO ARG LEU VAL SER GLY TYR ARG ARG SEQRES 4 A 105 ILE ILE LYS ASN PRO MET ASP PHE SER THR MET ARG GLU SEQRES 5 A 105 ARG LEU LEU ARG GLY GLY TYR THR SER SER GLU GLU PHE SEQRES 6 A 105 ALA ALA ASP ALA LEU LEU VAL PHE ASP ASN CYS GLN THR SEQRES 7 A 105 PHE ASN GLU ASP ASP SER GLU VAL GLY LYS ALA GLY HIS SEQRES 8 A 105 ILE MET ARG ARG PHE PHE GLU SER ARG TRP GLU GLU PHE SEQRES 9 A 105 TYR HET 6RZ A1901 30 HETNAM 6RZ 2-METHYL-~{N}-[(2~{R})-1-METHYLSULFONYLPROPAN-2- HETNAM 2 6RZ YL]PYRIDIN-3-AMINE FORMUL 2 6RZ C10 H16 N2 O2 S FORMUL 3 HOH *96(H2 O) HELIX 1 AA1 HIS A 1796 SER A 1811 1 16 HELIX 2 AA2 HIS A 1812 LEU A 1819 5 8 HELIX 3 AA3 GLY A 1829 ILE A 1834 1 6 HELIX 4 AA4 ASP A 1839 ARG A 1849 1 11 HELIX 5 AA5 SER A 1854 ASN A 1873 1 20 HELIX 6 AA6 SER A 1877 TYR A 1898 1 22 SITE 1 AC1 8 PRO A1817 GLU A1820 PRO A1821 VAL A1822 SITE 2 AC1 8 ASN A1823 PHE A1872 ASN A1873 HOH A2026 CRYST1 95.278 95.278 33.040 90.00 90.00 120.00 P 31 2 1 6 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 0.010496 0.006060 0.000000 0.00000 SCALE2 0.000000 0.012119 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030266 0.00000