HEADER GENE REGULATION 17-AUG-20 7JTC TITLE CRYSTAL STRUCTURE OF THE SECOND BROMODOMAIN (BD2) OF HUMAN TAF1 BOUND TITLE 2 TO ZS1-322 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CELL CYCLE GENE 1 PROTEIN,TBP-ASSOCIATED FACTOR 250 KDA, COMPND 5 P250,TRANSCRIPTION INITIATION FACTOR TFIID 250 KDA SUBUNIT,TAFII250; COMPND 6 EC: 2.3.1.48,2.7.11.1; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TAF1, BA2R, CCG1, CCGS, TAF2A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PNIC28.BSA4 KEYWDS BROMODOMAIN, TAF1, NON-BET, BET, KINASE INHIBITOR, ATR, DUAL BRD- KEYWDS 2 KINASE, GENE REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR M.R.KARIM,E.SCHONBRUNN REVDAT 2 18-OCT-23 7JTC 1 REMARK REVDAT 1 25-AUG-21 7JTC 0 JRNL AUTH M.R.KARIM,E.SCHONBRUNN JRNL TITL CRYSTAL STRUCTURE OF THE SECOND BROMODOMAIN (BD2) OF HUMAN JRNL TITL 2 TAF1 BOUND TO ZS1-322 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 10244 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 513 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 36.6400 - 3.2500 0.99 2542 134 0.1909 0.2070 REMARK 3 2 3.2500 - 2.5800 1.00 2427 128 0.2246 0.2757 REMARK 3 3 2.5800 - 2.2600 0.99 2392 126 0.1994 0.2356 REMARK 3 4 2.2600 - 2.0500 0.99 2370 125 0.2153 0.3024 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.250 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 45.88 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.78 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 1501 THROUGH 1539 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.0960 6.5487 -0.6181 REMARK 3 T TENSOR REMARK 3 T11: 0.2788 T22: 0.3745 REMARK 3 T33: 0.3916 T12: -0.1097 REMARK 3 T13: -0.0041 T23: 0.0265 REMARK 3 L TENSOR REMARK 3 L11: 3.9756 L22: 3.1792 REMARK 3 L33: 5.0471 L12: -2.8704 REMARK 3 L13: 1.8706 L23: -1.2907 REMARK 3 S TENSOR REMARK 3 S11: 0.0605 S12: -0.3854 S13: -0.3851 REMARK 3 S21: -0.1477 S22: 0.0159 S23: 0.2345 REMARK 3 S31: 0.5142 S32: -0.3626 S33: -0.0814 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1540 THROUGH 1587 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.0245 10.1255 -5.0555 REMARK 3 T TENSOR REMARK 3 T11: 0.2755 T22: 0.3114 REMARK 3 T33: 0.3090 T12: -0.0481 REMARK 3 T13: 0.0215 T23: -0.0206 REMARK 3 L TENSOR REMARK 3 L11: 3.7027 L22: 4.7252 REMARK 3 L33: 4.8590 L12: -2.0198 REMARK 3 L13: 1.0563 L23: -1.5795 REMARK 3 S TENSOR REMARK 3 S11: 0.1467 S12: 0.1102 S13: 0.0663 REMARK 3 S21: -0.3471 S22: -0.2206 S23: -0.0318 REMARK 3 S31: 0.3155 S32: 0.1764 S33: 0.0630 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1588 THROUGH 1607 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.7091 12.4262 7.7434 REMARK 3 T TENSOR REMARK 3 T11: 0.2905 T22: 0.4538 REMARK 3 T33: 0.3345 T12: -0.0562 REMARK 3 T13: 0.0169 T23: -0.0522 REMARK 3 L TENSOR REMARK 3 L11: 3.3614 L22: 6.2152 REMARK 3 L33: 4.9188 L12: -3.1823 REMARK 3 L13: 1.2546 L23: -0.7865 REMARK 3 S TENSOR REMARK 3 S11: -0.1063 S12: -0.6292 S13: -0.1142 REMARK 3 S21: 0.5493 S22: 0.1453 S23: 0.3679 REMARK 3 S31: 0.0655 S32: -0.3774 S33: 0.0881 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1608 THROUGH 1635 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.9935 -12.3608 -0.7315 REMARK 3 T TENSOR REMARK 3 T11: 0.8552 T22: 0.5620 REMARK 3 T33: 0.5174 T12: 0.2925 REMARK 3 T13: 0.0036 T23: 0.0915 REMARK 3 L TENSOR REMARK 3 L11: 2.2274 L22: 3.8953 REMARK 3 L33: 5.9336 L12: -1.3885 REMARK 3 L13: -1.8872 L23: 3.7432 REMARK 3 S TENSOR REMARK 3 S11: -0.4920 S12: -0.4186 S13: -0.3637 REMARK 3 S21: 0.6148 S22: 0.4878 S23: -0.1449 REMARK 3 S31: 1.4564 S32: 1.3973 S33: -0.0529 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 7JTC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-AUG-20. REMARK 100 THE DEPOSITION ID IS D_1000251324. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUL-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10246 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 36.640 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 6.453 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.0800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.82 REMARK 200 R MERGE FOR SHELL (I) : 0.78800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.090 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: 7JJG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.01 M CO(II) CHLORIDE, 0.1 M SODIUM REMARK 280 ACETATE TRIHYDRATE (PH 4.6), 1 M 1,6-HEXANEDIOL, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 23.30000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 29.64000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.44500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 29.64000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.30000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.44500 REMARK 290 SMTRY3 4 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: 250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 4.0 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 1499 REMARK 465 MET A 1500 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASP A1501 CG OD1 OD2 REMARK 470 LEU A1626 CG CD1 CD2 REMARK 470 LEU A1631 CG CD1 CD2 REMARK 470 GLU A1632 CG CD OE1 OE2 REMARK 470 ASP A1635 CG OD1 OD2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue VK1 A 1701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 1702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 1703 DBREF 7JTC A 1501 1635 UNP P21675 TAF1_HUMAN 1522 1656 SEQADV 7JTC SER A 1499 UNP P21675 EXPRESSION TAG SEQADV 7JTC MET A 1500 UNP P21675 EXPRESSION TAG SEQRES 1 A 137 SER MET ASP ASP ASP GLN VAL ALA PHE SER PHE ILE LEU SEQRES 2 A 137 ASP ASN ILE VAL THR GLN LYS MET MET ALA VAL PRO ASP SEQRES 3 A 137 SER TRP PRO PHE HIS HIS PRO VAL ASN LYS LYS PHE VAL SEQRES 4 A 137 PRO ASP TYR TYR LYS VAL ILE VAL ASN PRO MET ASP LEU SEQRES 5 A 137 GLU THR ILE ARG LYS ASN ILE SER LYS HIS LYS TYR GLN SEQRES 6 A 137 SER ARG GLU SER PHE LEU ASP ASP VAL ASN LEU ILE LEU SEQRES 7 A 137 ALA ASN SER VAL LYS TYR ASN GLY PRO GLU SER GLN TYR SEQRES 8 A 137 THR LYS THR ALA GLN GLU ILE VAL ASN VAL CYS TYR GLN SEQRES 9 A 137 THR LEU THR GLU TYR ASP GLU HIS LEU THR GLN LEU GLU SEQRES 10 A 137 LYS ASP ILE CYS THR ALA LYS GLU ALA ALA LEU GLU GLU SEQRES 11 A 137 ALA GLU LEU GLU SER LEU ASP HET VK1 A1701 22 HET EDO A1702 4 HET EDO A1703 4 HETNAM VK1 1-{6-[(3R)-3-METHYLMORPHOLIN-4-YL]-2-(METHYLSULFANYL) HETNAM 2 VK1 PYRIMIDIN-4-YL}CYCLOPROPANE-1-SULFONIMIDOAMIDE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 VK1 C13 H21 N5 O2 S2 FORMUL 3 EDO 2(C2 H6 O2) FORMUL 5 HOH *17(H2 O) HELIX 1 AA1 ASP A 1501 LYS A 1518 1 18 HELIX 2 AA2 SER A 1525 HIS A 1529 5 5 HELIX 3 AA3 ASP A 1539 ILE A 1544 1 6 HELIX 4 AA4 ASP A 1549 LYS A 1559 1 11 HELIX 5 AA5 SER A 1564 GLY A 1584 1 21 HELIX 6 AA6 SER A 1587 TYR A 1607 1 21 HELIX 7 AA7 TYR A 1607 LEU A 1634 1 28 SITE 1 AC1 8 PRO A1527 HIS A1530 PRO A1531 VAL A1532 SITE 2 AC1 8 ASN A1533 PHE A1536 ASN A1583 TYR A1601 SITE 1 AC2 4 ASP A1524 LYS A1561 ASP A1570 ASP A1571 SITE 1 AC3 5 ASP A1524 GLU A1566 ASP A1570 TYR A1589 SITE 2 AC3 5 THR A1592 CRYST1 46.600 56.890 59.280 90.00 90.00 90.00 P 21 21 21 4 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 0.021459 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017578 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016869 0.00000