HEADER TRANSCRIPTION 26-JAN-22 7QX9 TITLE BAZ2A BROMODOMAIN IN COMPLEX WITH ACETYLPYRROLE DERIVATIVE COMPOUND 65 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 MUTATION: YES 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,G.CAZZANELLI,A.CAFLISCH,G.LOLLI REVDAT 2 31-JAN-24 7QX9 1 REMARK REVDAT 1 28-SEP-22 7QX9 0 JRNL AUTH A.DALLE VEDOVE,G.CAZZANELLI,L.BATISTE,J.R.MARCHAND, JRNL AUTH 2 D.SPILIOTOPOULOS,J.CORSI,V.G.D'AGOSTINO,A.CAFLISCH,G.LOLLI JRNL TITL IDENTIFICATION OF A BAZ2A-BROMODOMAIN HIT COMPOUND BY JRNL TITL 2 FRAGMENT GROWING. JRNL REF ACS MED.CHEM.LETT. V. 13 1434 2022 JRNL REFN ISSN 1948-5875 JRNL PMID 36105334 JRNL DOI 10.1021/ACSMEDCHEMLETT.2C00173 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 15717 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.350 REMARK 3 FREE R VALUE TEST SET COUNT : 684 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 37.5420 - 2.5647 1.00 3086 117 0.1665 0.1851 REMARK 3 2 2.5647 - 2.0357 1.00 3038 114 0.1768 0.2059 REMARK 3 3 2.0357 - 1.7784 1.00 3022 114 0.1997 0.2297 REMARK 3 4 1.7784 - 1.6158 1.00 2954 166 0.2441 0.2988 REMARK 3 5 1.6158 - 1.5000 1.00 2933 173 0.2499 0.2719 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.780 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.65 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 : 0.009 939 REMARK 3 ANGLE : 1.045 1277 REMARK 3 CHIRALITY : 0.052 124 REMARK 3 PLANARITY : 0.006 170 REMARK 3 DIHEDRAL : 21.280 563 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1796 THROUGH 1810 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.6165 -1.8892 6.1956 REMARK 3 T TENSOR REMARK 3 T11: 0.1647 T22: 0.1473 REMARK 3 T33: 0.1547 T12: -0.0119 REMARK 3 T13: -0.0008 T23: 0.0298 REMARK 3 L TENSOR REMARK 3 L11: 0.0156 L22: -0.0014 REMARK 3 L33: 0.0067 L12: 0.0113 REMARK 3 L13: 0.0012 L23: 0.0122 REMARK 3 S TENSOR REMARK 3 S11: 0.1475 S12: 0.1009 S13: 0.0403 REMARK 3 S21: -0.1910 S22: -0.0617 S23: -0.0093 REMARK 3 S31: -0.1136 S32: -0.0044 S33: -0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1811 THROUGH 1829 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.4066 -5.2045 25.9578 REMARK 3 T TENSOR REMARK 3 T11: 0.1349 T22: 0.1827 REMARK 3 T33: 0.1268 T12: 0.0021 REMARK 3 T13: 0.0113 T23: 0.0016 REMARK 3 L TENSOR REMARK 3 L11: 0.2451 L22: 0.2633 REMARK 3 L33: 0.3550 L12: -0.2078 REMARK 3 L13: 0.1959 L23: -0.0080 REMARK 3 S TENSOR REMARK 3 S11: -0.1433 S12: -0.2897 S13: 0.3360 REMARK 3 S21: 0.0004 S22: -0.0482 S23: -0.2561 REMARK 3 S31: -0.2099 S32: -0.0133 S33: -0.0473 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1830 THROUGH 1839 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.5293 -16.7279 23.8494 REMARK 3 T TENSOR REMARK 3 T11: 0.1542 T22: 0.1419 REMARK 3 T33: 0.1606 T12: -0.0072 REMARK 3 T13: -0.0067 T23: 0.0469 REMARK 3 L TENSOR REMARK 3 L11: 0.0169 L22: 0.0211 REMARK 3 L33: 0.0340 L12: -0.0107 REMARK 3 L13: -0.0184 L23: 0.0260 REMARK 3 S TENSOR REMARK 3 S11: -0.0562 S12: -0.1597 S13: -0.1221 REMARK 3 S21: -0.0089 S22: 0.1133 S23: -0.0814 REMARK 3 S31: 0.0169 S32: -0.0632 S33: 0.0078 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1840 THROUGH 1854 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.6011 -9.4957 11.6808 REMARK 3 T TENSOR REMARK 3 T11: 0.1601 T22: 0.1431 REMARK 3 T33: 0.1543 T12: 0.0362 REMARK 3 T13: 0.0185 T23: 0.0341 REMARK 3 L TENSOR REMARK 3 L11: 0.0483 L22: 0.1549 REMARK 3 L33: 0.3388 L12: -0.0527 REMARK 3 L13: -0.0929 L23: 0.2242 REMARK 3 S TENSOR REMARK 3 S11: 0.1135 S12: 0.1060 S13: -0.0836 REMARK 3 S21: 0.0106 S22: -0.2228 S23: -0.1190 REMARK 3 S31: 0.1265 S32: -0.0075 S33: -0.0266 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1855 THROUGH 1872 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.2095 -11.7275 14.4831 REMARK 3 T TENSOR REMARK 3 T11: 0.1256 T22: 0.1168 REMARK 3 T33: 0.1397 T12: -0.0011 REMARK 3 T13: -0.0016 T23: 0.0075 REMARK 3 L TENSOR REMARK 3 L11: 0.0293 L22: 0.1360 REMARK 3 L33: 0.0130 L12: -0.0622 REMARK 3 L13: 0.0029 L23: -0.0254 REMARK 3 S TENSOR REMARK 3 S11: 0.0535 S12: 0.0204 S13: -0.0835 REMARK 3 S21: -0.1328 S22: -0.0548 S23: 0.0801 REMARK 3 S31: -0.0635 S32: -0.1684 S33: -0.0018 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1873 THROUGH 1898 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.3895 -3.0195 13.4718 REMARK 3 T TENSOR REMARK 3 T11: 0.1469 T22: 0.1750 REMARK 3 T33: 0.1343 T12: 0.0459 REMARK 3 T13: -0.0113 T23: 0.0221 REMARK 3 L TENSOR REMARK 3 L11: 0.0596 L22: 0.1750 REMARK 3 L33: 0.0732 L12: -0.0467 REMARK 3 L13: 0.0302 L23: 0.0455 REMARK 3 S TENSOR REMARK 3 S11: 0.0145 S12: 0.0710 S13: 0.0204 REMARK 3 S21: -0.1112 S22: -0.0109 S23: 0.1527 REMARK 3 S31: -0.1548 S32: -0.1781 S33: -0.0036 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 7QX9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-JAN-22. REMARK 100 THE DEPOSITION ID IS D_1292120587. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-AUG-19 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 : 11.2C 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 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15741 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 37.542 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.08600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.30 REMARK 200 R MERGE FOR SHELL (I) : 0.71700 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 (%): 38.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 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 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 17.48050 REMARK 290 SMTRY3 2 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: 6490 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 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 SER A 1794 REMARK 465 MET A 1795 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7QVU RELATED DB: PDB REMARK 900 7QVU CONTAINS THE SAME PROTEIN COMPLEXED WITH A SIMILAR LIGAND. REMARK 900 RELATED ID: 7QWU RELATED DB: PDB REMARK 900 7QWU CONTAINS THE SAME PROTEIN COMPLEXED WITH A SIMILAR LIGAND. REMARK 900 RELATED ID: 7QWF RELATED DB: PDB REMARK 900 7QWF CONTAINS THE SAME PROTEIN COMPLEXED WITH A SIMILAR LIGAND. REMARK 900 RELATED ID: 7QWY RELATED DB: PDB REMARK 900 7QWY CONTAINS THE SAME PROTEIN COMPLEXED WITH A SIMILAR LIGAND. REMARK 900 RELATED ID: 7QX2 RELATED DB: PDB REMARK 900 7QX2 CONTAINS THE SAME PROTEIN COMPLEXED WITH A SIMILAR LIGAND. DBREF 7QX9 A 1796 1898 UNP Q9UIF9 BAZ2A_HUMAN 1796 1898 SEQADV 7QX9 SER A 1794 UNP Q9UIF9 EXPRESSION TAG SEQADV 7QX9 MET A 1795 UNP Q9UIF9 EXPRESSION TAG SEQADV 7QX9 HIS A 1845 UNP Q9UIF9 GLU 1845 ENGINEERED MUTATION SEQADV 7QX9 SER A 1848 UNP Q9UIF9 LEU 1848 ENGINEERED MUTATION SEQRES 1 A 105 SER MET 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 HIS SEQRES 5 A 105 ARG LEU SER 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 G2U A1901 39 HETNAM G2U 3-[[4-(4-ETHANOYL-3,5-DIMETHYL-1~{H}-PYRROL-2-YL)-1,3- HETNAM 2 G2U THIAZOL-2-YL]METHYL]IMIDAZOLIDINE-2,4-DIONE FORMUL 2 G2U C15 H16 N4 O3 S FORMUL 3 HOH *115(H2 O) HELIX 1 AA1 HIS A 1796 ASP A 1798 5 3 HELIX 2 AA2 LEU A 1799 SER A 1811 1 13 HELIX 3 AA3 ALA A 1815 LEU A 1819 5 5 HELIX 4 AA4 GLY A 1829 ILE A 1834 1 6 HELIX 5 AA5 ASP A 1839 ARG A 1849 1 11 HELIX 6 AA6 SER A 1854 ASN A 1873 1 20 HELIX 7 AA7 SER A 1877 GLU A 1895 1 19 CRYST1 37.528 34.961 37.562 90.00 91.88 90.00 P 1 21 1 2 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 0.026647 0.000000 0.000873 0.00000 SCALE2 0.000000 0.028603 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026637 0.00000