HEADER TRANSFERASE 23-MAY-19 6P39 TITLE CRYSTAL STRUCTURE ANALYSIS OF TAF1 BROMODOMAIN 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 KEYWDS KINASE, BROMODOMAIN, INHIBITOR, TRANSCRIPTION, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR H.-S.SEO,S.DHE-PAGANON REVDAT 2 11-OCT-23 6P39 1 REMARK REVDAT 1 27-MAY-20 6P39 0 JRNL AUTH H.-S.SEO,S.DHE-PAGANON JRNL TITL CRYSTAL STRUCTURE ANALYSIS OF TAF1 BROMODOMAIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.94 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.94 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 10763 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 536 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 42.6808 - 4.6662 1.00 2627 160 0.1588 0.1838 REMARK 3 2 4.6662 - 3.7044 1.00 2557 120 0.1852 0.2010 REMARK 3 3 3.7044 - 3.2363 1.00 2523 124 0.2573 0.3083 REMARK 3 4 3.2363 - 2.9405 1.00 2520 132 0.3305 0.3257 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.390 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.670 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 80.95 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 99.85 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 : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1521 THROUGH 1538 ) REMARK 3 ORIGIN FOR THE GROUP (A): 40.3735 -38.9077 -31.2615 REMARK 3 T TENSOR REMARK 3 T11: 0.7166 T22: 0.9041 REMARK 3 T33: 0.8203 T12: -0.2132 REMARK 3 T13: 0.0817 T23: 0.0566 REMARK 3 L TENSOR REMARK 3 L11: 9.2632 L22: 5.7359 REMARK 3 L33: 4.5521 L12: 1.7182 REMARK 3 L13: 4.1609 L23: 1.6487 REMARK 3 S TENSOR REMARK 3 S11: -0.5788 S12: 0.3401 S13: -0.9881 REMARK 3 S21: -1.0459 S22: 0.8785 S23: -0.1493 REMARK 3 S31: -0.9579 S32: 0.6193 S33: -0.3592 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1539 THROUGH 1552 ) REMARK 3 ORIGIN FOR THE GROUP (A): 47.2045 -30.0661 -15.2520 REMARK 3 T TENSOR REMARK 3 T11: 0.9103 T22: 0.9504 REMARK 3 T33: 0.9235 T12: -0.0646 REMARK 3 T13: -0.0742 T23: -0.0950 REMARK 3 L TENSOR REMARK 3 L11: 2.4131 L22: 7.6826 REMARK 3 L33: 7.0519 L12: -3.7286 REMARK 3 L13: 2.3921 L23: -3.2581 REMARK 3 S TENSOR REMARK 3 S11: -0.0196 S12: 0.1332 S13: 0.3874 REMARK 3 S21: 1.0008 S22: -0.2932 S23: -1.3758 REMARK 3 S31: -1.0472 S32: 1.5322 S33: -0.3323 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1553 THROUGH 1570 ) REMARK 3 ORIGIN FOR THE GROUP (A): 55.2322 -41.0460 -7.2119 REMARK 3 T TENSOR REMARK 3 T11: 0.9253 T22: 0.9565 REMARK 3 T33: 0.9157 T12: 0.0318 REMARK 3 T13: 0.0036 T23: -0.0327 REMARK 3 L TENSOR REMARK 3 L11: 7.0664 L22: 4.8288 REMARK 3 L33: 3.5189 L12: 1.4244 REMARK 3 L13: 2.2494 L23: 1.0184 REMARK 3 S TENSOR REMARK 3 S11: 0.2362 S12: 0.6572 S13: -0.2315 REMARK 3 S21: 0.6726 S22: 0.0980 S23: 0.3808 REMARK 3 S31: 0.2964 S32: 0.3888 S33: -0.8161 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1571 THROUGH 1579 ) REMARK 3 ORIGIN FOR THE GROUP (A): 48.9873 -40.1245 -23.0220 REMARK 3 T TENSOR REMARK 3 T11: 0.8018 T22: 1.0451 REMARK 3 T33: 0.9380 T12: -0.0659 REMARK 3 T13: -0.0030 T23: -0.1657 REMARK 3 L TENSOR REMARK 3 L11: 9.2352 L22: 3.5175 REMARK 3 L33: 3.1874 L12: -3.0920 REMARK 3 L13: -1.9404 L23: -1.9813 REMARK 3 S TENSOR REMARK 3 S11: -0.3904 S12: 0.9687 S13: -1.0048 REMARK 3 S21: -0.3037 S22: 0.3623 S23: -1.0260 REMARK 3 S31: -0.0459 S32: 1.2158 S33: -0.2648 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1580 THROUGH 1627 ) REMARK 3 ORIGIN FOR THE GROUP (A): 40.0547 -38.3312 -13.6410 REMARK 3 T TENSOR REMARK 3 T11: 0.8273 T22: 0.9744 REMARK 3 T33: 0.9246 T12: 0.0122 REMARK 3 T13: 0.0752 T23: 0.0192 REMARK 3 L TENSOR REMARK 3 L11: 6.1674 L22: 2.2218 REMARK 3 L33: 8.8733 L12: 1.6806 REMARK 3 L13: 3.7929 L23: 2.8314 REMARK 3 S TENSOR REMARK 3 S11: 0.1222 S12: -0.7969 S13: -0.0752 REMARK 3 S21: 0.3276 S22: -0.2934 S23: 0.2501 REMARK 3 S31: 0.4205 S32: -0.7538 S33: 0.1896 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1628 THROUGH 1648 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.8862 -48.0465 -32.5683 REMARK 3 T TENSOR REMARK 3 T11: 1.0030 T22: 1.0818 REMARK 3 T33: 1.1104 T12: -0.0689 REMARK 3 T13: 0.0704 T23: -0.0337 REMARK 3 L TENSOR REMARK 3 L11: 4.9101 L22: 2.5143 REMARK 3 L33: 2.5695 L12: 0.2565 REMARK 3 L13: 2.9236 L23: 1.1840 REMARK 3 S TENSOR REMARK 3 S11: 0.1496 S12: 0.4531 S13: -1.3661 REMARK 3 S21: 0.3266 S22: 0.0154 S23: 0.3312 REMARK 3 S31: 0.4625 S32: 0.2896 S33: 0.2069 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 6P39 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-MAY-19. REMARK 100 THE DEPOSITION ID IS D_1000241803. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-OCT-18 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 : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10784 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.940 REMARK 200 RESOLUTION RANGE LOW (A) : 45.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.94 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.99 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 10.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.400 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: 3UV5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG1000, TRIS PH 8.0, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K 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 30.37667 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 60.75333 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 60.75333 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 30.37667 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 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 1519 REMARK 465 MET A 1520 REMARK 465 GLU A 1649 REMARK 465 ALA A 1650 REMARK 465 GLU A 1651 REMARK 465 LEU A 1652 REMARK 465 GLU A 1653 REMARK 465 SER A 1654 REMARK 465 LEU A 1655 REMARK 465 ASP A 1656 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 LYS A1555 NZ REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NQY A 4000 DBREF 6P39 A 1521 1656 UNP P21675 TAF1_HUMAN 1521 1656 SEQADV 6P39 SER A 1519 UNP P21675 EXPRESSION TAG SEQADV 6P39 MET A 1520 UNP P21675 EXPRESSION TAG SEQRES 1 A 138 SER MET ASP ASP ASP ASP GLN VAL ALA PHE SER PHE ILE SEQRES 2 A 138 LEU ASP ASN ILE VAL THR GLN LYS MET MET ALA VAL PRO SEQRES 3 A 138 ASP SER TRP PRO PHE HIS HIS PRO VAL ASN LYS LYS PHE SEQRES 4 A 138 VAL PRO ASP TYR TYR LYS VAL ILE VAL ASN PRO MET ASP SEQRES 5 A 138 LEU GLU THR ILE ARG LYS ASN ILE SER LYS HIS LYS TYR SEQRES 6 A 138 GLN SER ARG GLU SER PHE LEU ASP ASP VAL ASN LEU ILE SEQRES 7 A 138 LEU ALA ASN SER VAL LYS TYR ASN GLY PRO GLU SER GLN SEQRES 8 A 138 TYR THR LYS THR ALA GLN GLU ILE VAL ASN VAL CYS TYR SEQRES 9 A 138 GLN THR LEU THR GLU TYR ASP GLU HIS LEU THR GLN LEU SEQRES 10 A 138 GLU LYS ASP ILE CYS THR ALA LYS GLU ALA ALA LEU GLU SEQRES 11 A 138 GLU ALA GLU LEU GLU SER LEU ASP HET NQY A4000 35 HETNAM NQY 3-METHOXY-4-{[(6AR)-5-METHYL-6-OXO-6,6A,7,8,9,10- HETNAM 2 NQY HEXAHYDRO-5H-DIPYRIDO[1,2-A:3',2'-E]PYRAZIN-2- HETNAM 3 NQY YL]AMINO}-N-(1-METHYLPIPERIDIN-4-YL)BENZAMIDE FORMUL 2 NQY C26 H34 N6 O3 HELIX 1 AA1 ASP A 1522 LYS A 1539 1 18 HELIX 2 AA2 SER A 1546 HIS A 1550 5 5 HELIX 3 AA3 ASP A 1560 ILE A 1565 1 6 HELIX 4 AA4 ASP A 1570 LYS A 1580 1 11 HELIX 5 AA5 SER A 1585 GLY A 1605 1 21 HELIX 6 AA6 SER A 1608 TYR A 1628 1 21 HELIX 7 AA7 TYR A 1628 GLU A 1648 1 21 SSBOND 1 CYS A 1640 CYS A 1640 1555 6554 2.02 SITE 1 AC1 10 ASP A1523 PHE A1530 TRP A1547 PRO A1548 SITE 2 AC1 10 VAL A1553 ASN A1554 PHE A1557 TYR A1603 SITE 3 AC1 10 ASN A1604 TYR A1610 CRYST1 96.600 96.600 91.130 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 0.010352 0.005977 0.000000 0.00000 SCALE2 0.000000 0.011953 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010973 0.00000