HEADER GENE REGULATION 07-JAN-21 7LB3 TITLE CRYSTAL STRUCTURE OF THE SECOND BROMODOMAIN (BD2) OF HUMAN TAF1 BOUND TITLE 2 TO ZS1-580 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SECOND BROMODOMAIN; COMPND 5 SYNONYM: CELL CYCLE GENE 1 PROTEIN,TBP-ASSOCIATED FACTOR 250 KDA, COMPND 6 P250,TRANSCRIPTION INITIATION FACTOR TFIID 250 KDA SUBUNIT,TAFII250; 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 KEYWDS BROMODOMAIN, TAF1, NON-BET, BET, KINASE INHIBITOR, ATR, DUAL BRD- KEYWDS 2 KINASE, TRANSFERASE, GENE REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR M.R.KARIM,E.SCHONBRUNN REVDAT 2 18-OCT-23 7LB3 1 REMARK REVDAT 1 12-JAN-22 7LB3 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 ZS1-580 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19_4085 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.11 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 12978 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.960 REMARK 3 FREE R VALUE TEST SET COUNT : 644 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 41.1100 - 3.2500 1.00 2588 133 0.1640 0.1685 REMARK 3 2 3.2500 - 2.5800 1.00 2463 129 0.1831 0.2302 REMARK 3 3 2.5800 - 2.2500 1.00 2450 130 0.2007 0.2261 REMARK 3 4 2.2500 - 2.0500 1.00 2410 125 0.2059 0.2067 REMARK 3 5 2.0500 - 1.9000 1.00 2423 127 0.3207 0.3655 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) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.550 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.21 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 1173 REMARK 3 ANGLE : 1.221 1596 REMARK 3 CHIRALITY : 0.065 177 REMARK 3 PLANARITY : 0.008 202 REMARK 3 DIHEDRAL : 9.592 154 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1499 THROUGH 1539 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.6601 5.4632 59.7019 REMARK 3 T TENSOR REMARK 3 T11: 0.1816 T22: 0.1783 REMARK 3 T33: 0.2043 T12: 0.0457 REMARK 3 T13: 0.0188 T23: 0.0188 REMARK 3 L TENSOR REMARK 3 L11: 3.2973 L22: 4.1933 REMARK 3 L33: 3.6786 L12: 2.2565 REMARK 3 L13: 2.1326 L23: 2.2611 REMARK 3 S TENSOR REMARK 3 S11: 0.1732 S12: -0.0021 S13: -0.2181 REMARK 3 S21: 0.2992 S22: -0.0987 S23: -0.1348 REMARK 3 S31: 0.5159 S32: 0.0100 S33: -0.0396 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1540 THROUGH 1607 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.6362 11.1017 60.4100 REMARK 3 T TENSOR REMARK 3 T11: 0.1259 T22: 0.1756 REMARK 3 T33: 0.1817 T12: 0.0339 REMARK 3 T13: 0.0222 T23: 0.0159 REMARK 3 L TENSOR REMARK 3 L11: 2.0713 L22: 3.1106 REMARK 3 L33: 2.6578 L12: 1.3906 REMARK 3 L13: 1.3380 L23: 1.4235 REMARK 3 S TENSOR REMARK 3 S11: 0.0099 S12: 0.0296 S13: 0.0808 REMARK 3 S21: 0.0828 S22: -0.0498 S23: -0.0058 REMARK 3 S31: 0.1269 S32: 0.0011 S33: 0.0550 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1608 THROUGH 1635 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.8101 -12.3324 60.7282 REMARK 3 T TENSOR REMARK 3 T11: 0.4023 T22: 0.3075 REMARK 3 T33: 0.2930 T12: -0.0718 REMARK 3 T13: 0.0003 T23: -0.0386 REMARK 3 L TENSOR REMARK 3 L11: 7.4214 L22: 4.8345 REMARK 3 L33: 7.3261 L12: 5.1106 REMARK 3 L13: -6.2804 L23: -2.9687 REMARK 3 S TENSOR REMARK 3 S11: -0.0792 S12: 0.1996 S13: -0.0005 REMARK 3 S21: 0.0114 S22: 0.3625 S23: 0.3163 REMARK 3 S31: 0.6317 S32: -0.7400 S33: 0.0292 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 7LB3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JAN-21. REMARK 100 THE DEPOSITION ID IS D_1000253817. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-DEC-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5417 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.1 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13028 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 41.110 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 1.51000 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: 7JSP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.15 M MGCL2, 0.1 M BIS-TRIS PH 5.5, REMARK 280 15% PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 23.37750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 29.53450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.61950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 29.53450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.37750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.61950 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 1803 O HOH A 1811 1.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 1856 O HOH A 1919 4547 2.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue XXS 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 DBREF 7LB3 A 1501 1635 UNP P21675 TAF1_HUMAN 1501 1635 SEQADV 7LB3 SER A 1499 UNP P21675 EXPRESSION TAG SEQADV 7LB3 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 XXS A1701 29 HET EDO A1702 4 HETNAM XXS 4-{4-[(3R)-3-METHYLMORPHOLIN-4-YL]-6-[1-(S- HETNAM 2 XXS METHYLSULFONIMIDOYL)CYCLOPROPYL]PYRIMIDIN-2-YL}-1H- HETNAM 3 XXS INDAZOLE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 XXS C20 H24 N6 O2 S FORMUL 3 EDO C2 H6 O2 FORMUL 4 HOH *154(H2 O) HELIX 1 AA1 SER A 1499 LYS A 1518 1 20 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 15 TRP A1526 PRO A1527 HIS A1530 PRO A1531 SITE 2 AC1 15 VAL A1532 ASN A1533 PHE A1536 ASN A1583 SITE 3 AC1 15 TYR A1589 TYR A1601 THR A1605 EDO A1702 SITE 4 AC1 15 HOH A1824 HOH A1825 HOH A1894 SITE 1 AC2 6 ARG A1565 ASP A1608 XXS A1701 HOH A1802 SITE 2 AC2 6 HOH A1806 HOH A1822 CRYST1 46.755 57.239 59.069 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 0.021388 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017471 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016929 0.00000