HEADER TRANSCRIPTION 29-JAN-22 7QYU TITLE BAZ2A BROMODOMAIN IN COMPLEX WITH ACETYLPYRROLE DERIVATIVE COMPOUND 88 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 7QYU 1 REMARK REVDAT 1 28-SEP-22 7QYU 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) : 27.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 15790 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.330 REMARK 3 FREE R VALUE TEST SET COUNT : 683 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 27.0790 - 2.5644 0.99 3142 91 0.1406 0.1845 REMARK 3 2 2.5644 - 2.0357 1.00 3077 103 0.1496 0.1665 REMARK 3 3 2.0357 - 1.7784 0.99 2989 159 0.1730 0.2132 REMARK 3 4 1.7784 - 1.6158 0.99 2917 198 0.2059 0.2563 REMARK 3 5 1.6158 - 1.5000 0.98 2982 132 0.2406 0.2523 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.200 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.99 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 : 0.008 959 REMARK 3 ANGLE : 1.040 1303 REMARK 3 CHIRALITY : 0.048 126 REMARK 3 PLANARITY : 0.006 173 REMARK 3 DIHEDRAL : 23.267 580 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 1794 THROUGH 1811 ) REMARK 3 ORIGIN FOR THE GROUP (A): -12.2589 1.2182 -1.0283 REMARK 3 T TENSOR REMARK 3 T11: 0.1953 T22: 0.1546 REMARK 3 T33: 0.2226 T12: 0.0020 REMARK 3 T13: 0.0006 T23: -0.0008 REMARK 3 L TENSOR REMARK 3 L11: 0.6358 L22: 0.4219 REMARK 3 L33: 0.4435 L12: -0.0492 REMARK 3 L13: 0.1711 L23: -0.3916 REMARK 3 S TENSOR REMARK 3 S11: 0.0639 S12: -0.1288 S13: -0.1140 REMARK 3 S21: -0.0338 S22: 0.0549 S23: 0.0938 REMARK 3 S31: 0.0102 S32: -0.0132 S33: -0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1812 THROUGH 1839 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.1968 9.6987 -7.0395 REMARK 3 T TENSOR REMARK 3 T11: 0.1842 T22: 0.1823 REMARK 3 T33: 0.1789 T12: 0.0215 REMARK 3 T13: 0.0075 T23: 0.0087 REMARK 3 L TENSOR REMARK 3 L11: 1.4956 L22: 0.8855 REMARK 3 L33: 1.7329 L12: 0.1554 REMARK 3 L13: -0.0604 L23: 0.5454 REMARK 3 S TENSOR REMARK 3 S11: 0.0448 S12: 0.3312 S13: 0.0139 REMARK 3 S21: 0.0021 S22: -0.0261 S23: 0.0037 REMARK 3 S31: 0.0057 S32: 0.0624 S33: 0.0001 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1840 THROUGH 1854 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.3572 8.5614 1.5400 REMARK 3 T TENSOR REMARK 3 T11: 0.2046 T22: 0.1428 REMARK 3 T33: 0.2465 T12: -0.0079 REMARK 3 T13: 0.0077 T23: -0.0241 REMARK 3 L TENSOR REMARK 3 L11: 0.3120 L22: 0.2036 REMARK 3 L33: 0.2772 L12: 0.0056 REMARK 3 L13: 0.0308 L23: -0.2657 REMARK 3 S TENSOR REMARK 3 S11: 0.0419 S12: -0.1400 S13: 0.2514 REMARK 3 S21: -0.0123 S22: 0.0595 S23: 0.1690 REMARK 3 S31: -0.0517 S32: -0.0696 S33: 0.0001 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1855 THROUGH 1872 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.6390 10.7861 -11.3781 REMARK 3 T TENSOR REMARK 3 T11: 0.2027 T22: 0.2499 REMARK 3 T33: 0.1803 T12: -0.0097 REMARK 3 T13: 0.0034 T23: 0.0253 REMARK 3 L TENSOR REMARK 3 L11: 0.5258 L22: 0.5927 REMARK 3 L33: 0.5178 L12: 0.4017 REMARK 3 L13: 0.2971 L23: -0.1662 REMARK 3 S TENSOR REMARK 3 S11: -0.0182 S12: 0.5934 S13: 0.0683 REMARK 3 S21: -0.0236 S22: 0.0558 S23: 0.1037 REMARK 3 S31: -0.0537 S32: -0.0292 S33: -0.0000 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1873 THROUGH 1898 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.2935 1.8640 -15.7274 REMARK 3 T TENSOR REMARK 3 T11: 0.2273 T22: 0.3757 REMARK 3 T33: 0.1594 T12: 0.0034 REMARK 3 T13: -0.0091 T23: -0.0889 REMARK 3 L TENSOR REMARK 3 L11: 0.6967 L22: 1.7098 REMARK 3 L33: 1.1871 L12: -0.9791 REMARK 3 L13: 0.0519 L23: 0.5895 REMARK 3 S TENSOR REMARK 3 S11: -0.0568 S12: 0.8947 S13: -0.5249 REMARK 3 S21: -0.1351 S22: -0.0405 S23: 0.1234 REMARK 3 S31: 0.1296 S32: 0.0068 S33: 0.0068 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 7QYU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-FEB-22. REMARK 100 THE DEPOSITION ID IS D_1292120656. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-FEB-20 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) : 0.9429 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 : 15823 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 37.830 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.1000 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 (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : 0.73400 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 (%): 38.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 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 17.73250 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: 6570 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 DBREF 7QYU A 1796 1898 UNP Q9UIF9 BAZ2A_HUMAN 1796 1898 SEQADV 7QYU SER A 1794 UNP Q9UIF9 EXPRESSION TAG SEQADV 7QYU MET A 1795 UNP Q9UIF9 EXPRESSION TAG SEQADV 7QYU HIS A 1845 UNP Q9UIF9 GLU 1845 ENGINEERED MUTATION SEQADV 7QYU 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 GJC A1901 60 HETNAM GJC 2-[4-[[4-[4-(4-ETHANOYL-3-ETHYL-5-METHYL-1~{H}-PYRROL- HETNAM 2 GJC 2-YL)-1,3-THIAZOL-2-YL]PIPERAZIN-1-YL]METHYL]-1,2,3- HETNAM 3 GJC TRIAZOL-1-YL]ETHANAMIDE FORMUL 2 GJC C21 H28 N8 O2 S FORMUL 3 HOH *146(H2 O) HELIX 1 AA1 HIS A 1796 ASP A 1798 5 3 HELIX 2 AA2 LEU A 1799 HIS A 1812 1 14 HELIX 3 AA3 ASP A 1813 LEU A 1819 5 7 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 TYR A 1898 1 22 CRYST1 37.127 35.465 37.864 90.00 92.49 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 0.026935 0.000000 0.001171 0.00000 SCALE2 0.000000 0.028197 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026435 0.00000