HEADER TRANSCRIPTION 31-JAN-22 7QZB TITLE BAZ2A BROMODOMAIN IN COMPLEX WITH ACETYLPYRROLE DERIVATIVE COMPOUND 98 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 7QZB 1 REMARK REVDAT 1 28-SEP-22 7QZB 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. 2.15 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 9354 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.840 REMARK 3 FREE R VALUE TEST SET COUNT : 359 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 47.0990 - 3.1015 1.00 3082 117 0.1559 0.1806 REMARK 3 2 3.1015 - 2.4618 1.00 2991 120 0.2036 0.2411 REMARK 3 3 2.4618 - 2.1510 0.99 2922 122 0.2135 0.2740 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) : 23.020 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.83 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 : 0.006 900 REMARK 3 ANGLE : 0.870 1214 REMARK 3 CHIRALITY : 0.043 117 REMARK 3 PLANARITY : 0.004 159 REMARK 3 DIHEDRAL : 18.554 529 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 1840 THROUGH 1872 ) REMARK 3 ORIGIN FOR THE GROUP (A): -29.4601 25.4111 -2.2507 REMARK 3 T TENSOR REMARK 3 T11: 0.3151 T22: 0.3604 REMARK 3 T33: 0.3319 T12: -0.0996 REMARK 3 T13: 0.0458 T23: -0.0077 REMARK 3 L TENSOR REMARK 3 L11: 1.1714 L22: 3.3077 REMARK 3 L33: 2.4679 L12: 1.2878 REMARK 3 L13: -0.6989 L23: -0.9228 REMARK 3 S TENSOR REMARK 3 S11: -0.2593 S12: 0.0082 S13: -0.3097 REMARK 3 S21: -0.4609 S22: 0.0447 S23: -0.4867 REMARK 3 S31: 0.4938 S32: -0.1272 S33: 0.1145 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1873 THROUGH 1898 ) REMARK 3 ORIGIN FOR THE GROUP (A): -27.5184 34.4237 7.2115 REMARK 3 T TENSOR REMARK 3 T11: 0.2215 T22: 0.4095 REMARK 3 T33: 0.2502 T12: -0.1037 REMARK 3 T13: -0.0274 T23: 0.0294 REMARK 3 L TENSOR REMARK 3 L11: 1.6701 L22: 5.2514 REMARK 3 L33: 3.8014 L12: -0.1931 REMARK 3 L13: 0.6787 L23: -0.5361 REMARK 3 S TENSOR REMARK 3 S11: 0.0650 S12: -0.4815 S13: -0.2021 REMARK 3 S21: 0.0039 S22: -0.0974 S23: -0.3501 REMARK 3 S31: 0.3703 S32: -0.2240 S33: 0.1548 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1797 THROUGH 1818 ) REMARK 3 ORIGIN FOR THE GROUP (A): -34.3633 25.6562 6.7011 REMARK 3 T TENSOR REMARK 3 T11: 0.3474 T22: 0.4824 REMARK 3 T33: 0.3726 T12: -0.1508 REMARK 3 T13: 0.0305 T23: 0.0372 REMARK 3 L TENSOR REMARK 3 L11: 1.3729 L22: 5.2947 REMARK 3 L33: 3.1265 L12: 0.2953 REMARK 3 L13: -0.5673 L23: -0.5134 REMARK 3 S TENSOR REMARK 3 S11: 0.2652 S12: -0.1880 S13: -0.5528 REMARK 3 S21: 0.3237 S22: -0.6466 S23: 0.4461 REMARK 3 S31: 0.6370 S32: -0.2988 S33: 0.2936 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1819 THROUGH 1829 ) REMARK 3 ORIGIN FOR THE GROUP (A): -38.5156 37.4966 -10.2830 REMARK 3 T TENSOR REMARK 3 T11: 0.2422 T22: 0.5075 REMARK 3 T33: 0.3313 T12: -0.0138 REMARK 3 T13: -0.0127 T23: -0.0250 REMARK 3 L TENSOR REMARK 3 L11: 1.7822 L22: 0.9697 REMARK 3 L33: 3.7734 L12: -0.8137 REMARK 3 L13: 2.3894 L23: -0.5546 REMARK 3 S TENSOR REMARK 3 S11: 0.0037 S12: 0.2603 S13: 0.2213 REMARK 3 S21: -0.1196 S22: -0.0448 S23: 0.3127 REMARK 3 S31: -0.0988 S32: -0.3369 S33: -0.3016 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1830 THROUGH 1839 ) REMARK 3 ORIGIN FOR THE GROUP (A): -29.5937 35.2233 -11.5561 REMARK 3 T TENSOR REMARK 3 T11: 0.2737 T22: 0.3895 REMARK 3 T33: 0.2265 T12: -0.1188 REMARK 3 T13: -0.0012 T23: -0.0362 REMARK 3 L TENSOR REMARK 3 L11: 2.1844 L22: 7.3783 REMARK 3 L33: 4.4288 L12: -0.1123 REMARK 3 L13: -0.2226 L23: -2.5518 REMARK 3 S TENSOR REMARK 3 S11: -0.2452 S12: 0.1135 S13: -0.3078 REMARK 3 S21: -0.9592 S22: -0.1508 S23: -0.2043 REMARK 3 S31: 0.6232 S32: -0.5533 S33: 0.1433 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 7QZB 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_1292120675. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAY-21 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 : 9370 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 81.580 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 16.70 REMARK 200 R MERGE (I) : 0.17700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : 14.00 REMARK 200 R MERGE FOR SHELL (I) : 1.48900 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 (%): 64.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.43 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 11.02933 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 22.05867 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 22.05867 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 11.02933 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: 230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 3.0 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 465 HIS A 1796 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7QYU RELATED DB: PDB REMARK 900 7QYU CONTAINS THE SAME PROTEIN COMPLEXED WITH A SIMILAR LIGAND. REMARK 900 RELATED ID: 7QZ4 RELATED DB: PDB REMARK 900 7QZ4 CONTAINS THE SAME PROTEIN COMPLEXED WITH A SIMILAR LIGAND. DBREF 7QZB A 1796 1898 UNP Q9UIF9 BAZ2A_HUMAN 1796 1898 SEQADV 7QZB SER A 1794 UNP Q9UIF9 EXPRESSION TAG SEQADV 7QZB MET A 1795 UNP Q9UIF9 EXPRESSION TAG SEQADV 7QZB HIS A 1845 UNP Q9UIF9 GLU 1845 ENGINEERED MUTATION SEQADV 7QZB 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 EDO A1901 4 HET GI0 A1902 29 HETNAM EDO 1,2-ETHANEDIOL HETNAM GI0 3-METHYL-1-[2-[4-[(4-METHYL-1~{H}-PYRAZOL-3-YL) HETNAM 2 GI0 METHYL]PIPERAZIN-1-YL]-1,3-THIAZOL-4-YL]-2,5,6,7- HETNAM 3 GI0 TETRAHYDROISOINDOL-4-ONE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO C2 H6 O2 FORMUL 3 GI0 C21 H26 N6 O S FORMUL 4 HOH *61(H2 O) HELIX 1 AA1 SER A 1797 SER A 1811 1 15 HELIX 2 AA2 HIS A 1812 LEU A 1819 5 8 HELIX 3 AA3 ASN A 1823 VAL A 1827 5 5 HELIX 4 AA4 GLY A 1829 ILE A 1834 1 6 HELIX 5 AA5 ASP A 1839 GLY A 1850 1 12 HELIX 6 AA6 SER A 1854 ASN A 1873 1 20 HELIX 7 AA7 SER A 1877 GLU A 1896 1 20 CRYST1 94.199 94.199 33.088 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 0.010616 0.006129 0.000000 0.00000 SCALE2 0.000000 0.012258 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030222 0.00000