HEADER TRANSCRIPTION 10-DEC-20 7B7G TITLE BAZ2A BROMODOMAIN IN COMPLEX WITH COMPOUNDS MS04 AND B11 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS FOUR HELICAL BUNDLE, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR A.DALLE VEDOVE,G.CAZZANELLI,M.SEDYKH,A.CAFLISCH,G.LOLLI REVDAT 3 31-JAN-24 7B7G 1 REMARK REVDAT 2 28-SEP-22 7B7G 1 JRNL REVDAT 1 20-OCT-21 7B7G 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 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.DALLE VEDOVE,G.CAZZANELLI,J.CORSI,M.SEDYKH,V.G.D'AGOSTINO, REMARK 1 AUTH 2 A.CAFLISCH,G.LOLLI REMARK 1 TITL IDENTIFICATION OF A BAZ2A BROMODOMAIN HIT COMPOUND BY REMARK 1 TITL 2 FRAGMENT JOINING REMARK 1 REF ACS BIO MED CHEM AU 2021 REMARK 1 REFN ESSN 2694-2437 REMARK 1 DOI 10.1021/ACSBIOMEDCHEMAU.1C00016 REMARK 2 REMARK 2 RESOLUTION. 1.43 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) : 1.43 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 18141 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.135 REMARK 3 R VALUE (WORKING SET) : 0.134 REMARK 3 FREE R VALUE : 0.161 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.820 REMARK 3 FREE R VALUE TEST SET COUNT : 875 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 37.7610 - 2.5951 1.00 2997 139 0.1492 0.1593 REMARK 3 2 2.5951 - 2.0598 0.99 2924 145 0.1364 0.1592 REMARK 3 3 2.0598 - 1.7995 0.99 2867 159 0.1233 0.1678 REMARK 3 4 1.7995 - 1.6349 0.98 2909 86 0.1178 0.1439 REMARK 3 5 1.6349 - 1.5177 0.98 2812 156 0.1079 0.1626 REMARK 3 6 1.5177 - 1.4283 0.96 2757 190 0.1077 0.1682 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.780 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.68 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 : 0.008 992 REMARK 3 ANGLE : 0.942 1351 REMARK 3 CHIRALITY : 0.067 131 REMARK 3 PLANARITY : 0.005 177 REMARK 3 DIHEDRAL : 28.382 379 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 7B7G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-DEC-20. REMARK 100 THE DEPOSITION ID IS D_1292112883. 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 : AIMLESS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18149 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.428 REMARK 200 RESOLUTION RANGE LOW (A) : 37.761 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.43 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.20000 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 (%): 39.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 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 17.65100 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 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 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue T1B A 1901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue T1E A 1902 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7B7B RELATED DB: PDB REMARK 900 7B7B CONTAINS THE SAME PROTEINS WITH A MISSING LIGAND DBREF 7B7G A 1796 1898 UNP Q9UIF9 BAZ2A_HUMAN 1796 1898 SEQADV 7B7G SER A 1794 UNP Q9UIF9 EXPRESSION TAG SEQADV 7B7G MET A 1795 UNP Q9UIF9 EXPRESSION TAG SEQADV 7B7G HIS A 1845 UNP Q9UIF9 GLU 1845 ENGINEERED MUTATION SEQADV 7B7G 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 T1B A1901 17 HET T1E A1902 22 HETNAM T1B 5-ETHYL-2-(3-METHYL-1,2,3-TRIAZOL-4-YL)-1~{H}- HETNAM 2 T1B BENZIMIDAZOLE HETNAM T1E 1-[1-(3,5-DIMETHOXYPHENYL)PIPERIDIN-4-YL]-2,3-DIMETHYL- HETNAM 2 T1E GUANIDINE FORMUL 2 T1B C12 H13 N5 FORMUL 3 T1E C16 H26 N4 O2 FORMUL 4 HOH *137(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 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 GLU A 1896 1 20 SITE 1 AC1 8 PRO A1817 VAL A1822 VAL A1827 ASN A1873 SITE 2 AC1 8 VAL A1879 T1E A1902 HOH A2012 HOH A2106 SITE 1 AC2 6 TRP A1816 PHE A1897 TYR A1898 T1B A1901 SITE 2 AC2 6 HOH A2024 HOH A2025 CRYST1 37.424 35.302 37.802 90.00 92.66 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 0.026721 0.000000 0.001243 0.00000 SCALE2 0.000000 0.028327 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026482 0.00000