HEADER NUCLEAR PROTEIN 13-AUG-15 5D7E TITLE CRYSTAL STRUCTURE OF TAF14 YEATS DOMAIN IN COMPLEX WITH H3K9AC COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 14; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ACTIN NON-COMPLEMENTING MUTANT 1,CHROMOSOME STABILITY COMPND 5 PROTEIN 10,SWI/SNF CHROMATIN-REMODELING COMPLEX SUBUNIT TAF14,SWI/SNF COMPND 6 COMPLEX 29 KDA SUBUNIT,SWI/SNF COMPLEX SUBUNIT TAF14,TBP-ASSOCIATED COMPND 7 FACTOR 14,TBP-ASSOCIATED FACTOR 30 KDA,TRANSCRIPTION FACTOR G 30 KDA COMPND 8 SUBUNIT,TRANSCRIPTION INITIATION FACTOR TFIIF 30 KDA SUBUNIT; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: H3K9AC; COMPND 12 CHAIN: C; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / SOURCE 3 S288C); SOURCE 4 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 5 ORGANISM_TAXID: 559292; SOURCE 6 STRAIN: ATCC 204508 / S288C; SOURCE 7 GENE: TAF14, ANC1, CST10, SWP29, TAF30, TFG3, YPL129W; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 13 ORGANISM_TAXID: 4932 KEYWDS ACETYLATION HISTONE YEATS READER, NUCLEAR PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR F.H.ANDREWS,E.K.SHANLE,B.D.STRAHL,T.G.KUTATELADZE REVDAT 3 11-DEC-19 5D7E 1 REMARK REVDAT 2 20-SEP-17 5D7E 1 JRNL REMARK REVDAT 1 23-SEP-15 5D7E 0 JRNL AUTH E.K.SHANLE,F.H.ANDREWS,H.MERIESH,S.L.MCDANIEL,R.DRONAMRAJU, JRNL AUTH 2 J.V.DIFIORE,D.JHA,G.G.WOZNIAK,J.B.BRIDGERS,J.L.KERSCHNER, JRNL AUTH 3 K.KRAJEWSKI,G.M.MARTIN,A.J.MORRISON,T.G.KUTATELADZE, JRNL AUTH 4 B.D.STRAHL JRNL TITL ASSOCIATION OF TAF14 WITH ACETYLATED HISTONE H3 DIRECTS GENE JRNL TITL 2 TRANSCRIPTION AND THE DNA DAMAGE RESPONSE. JRNL REF GENES DEV. V. 29 1795 2015 JRNL REFN ISSN 0890-9369 JRNL PMID 26341557 JRNL DOI 10.1101/GAD.269977.115 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.2_1309 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) : 56.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 15750 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 792 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 0.0000 - 3.4524 1.00 2594 140 0.1746 0.1924 REMARK 3 2 3.4524 - 2.7402 1.00 2521 133 0.1923 0.2327 REMARK 3 3 2.7402 - 2.3938 1.00 2463 134 0.1899 0.2247 REMARK 3 4 2.3938 - 2.1750 1.00 2476 126 0.1900 0.2502 REMARK 3 5 2.1750 - 2.0191 1.00 2456 132 0.1840 0.2291 REMARK 3 6 2.0191 - 1.9000 1.00 2448 127 0.2119 0.2848 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) : 23.600 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 1273 REMARK 3 ANGLE : 1.220 1725 REMARK 3 CHIRALITY : 0.052 191 REMARK 3 PLANARITY : 0.005 223 REMARK 3 DIHEDRAL : 13.501 493 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 43.7059 13.7370 1.3062 REMARK 3 T TENSOR REMARK 3 T11: 0.2380 T22: 0.1983 REMARK 3 T33: 0.2042 T12: 0.0392 REMARK 3 T13: -0.0064 T23: -0.0402 REMARK 3 L TENSOR REMARK 3 L11: 2.0994 L22: 5.9918 REMARK 3 L33: 0.9006 L12: -2.4508 REMARK 3 L13: 0.5902 L23: -0.7938 REMARK 3 S TENSOR REMARK 3 S11: 0.0866 S12: 0.0594 S13: 0.0525 REMARK 3 S21: -0.0932 S22: -0.1194 S23: 0.2075 REMARK 3 S31: -0.1037 S32: -0.1338 S33: 0.0464 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 5D7E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000212749. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-NOV-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 4.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NOIR-1 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15763 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 56.520 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.20 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : 0.04800 REMARK 200 FOR THE DATA SET : 30.8000 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) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.70 REMARK 200 R MERGE FOR SHELL (I) : 0.66000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM CITRATE AND 48% PEG600 REMARK 280 (V/V), PH 5.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 17.68267 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 8.84133 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 13.26200 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 4.42067 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 22.10333 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 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 ALA C 3 N CB REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ALA A 3 49.83 -85.83 REMARK 500 PRO A 60 0.90 -68.74 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 PEG A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MES A 204 DBREF 5D7E A 1 137 UNP P35189 TAF14_YEAST 1 137 DBREF 5D7E C 3 10 PDB 5D7E 5D7E 3 10 SEQADV 5D7E LEU A -2 UNP P35189 EXPRESSION TAG SEQADV 5D7E GLY A -1 UNP P35189 EXPRESSION TAG SEQADV 5D7E SER A 0 UNP P35189 EXPRESSION TAG SEQRES 1 A 140 LEU GLY SER MET VAL ALA THR VAL LYS ARG THR ILE ARG SEQRES 2 A 140 ILE LYS THR GLN GLN HIS ILE LEU PRO GLU VAL PRO PRO SEQRES 3 A 140 VAL GLU ASN PHE PRO VAL ARG GLN TRP SER ILE GLU ILE SEQRES 4 A 140 VAL LEU LEU ASP ASP GLU GLY LYS GLU ILE PRO ALA THR SEQRES 5 A 140 ILE PHE ASP LYS VAL ILE TYR HIS LEU HIS PRO THR PHE SEQRES 6 A 140 ALA ASN PRO ASN ARG THR PHE THR ASP PRO PRO PHE ARG SEQRES 7 A 140 ILE GLU GLU GLN GLY TRP GLY GLY PHE PRO LEU ASP ILE SEQRES 8 A 140 SER VAL PHE LEU LEU GLU LYS ALA GLY GLU ARG LYS ILE SEQRES 9 A 140 PRO HIS ASP LEU ASN PHE LEU GLN GLU SER TYR GLU VAL SEQRES 10 A 140 GLU HIS VAL ILE GLN ILE PRO LEU ASN LYS PRO LEU LEU SEQRES 11 A 140 THR GLU GLU LEU ALA LYS SER GLY SER THR SEQRES 1 C 8 ALA GLN THR ALA ARG ALY SER THR HET ALY C 8 12 HET PEG A 201 7 HET PEG A 202 7 HET PEG A 203 7 HET MES A 204 12 HETNAM ALY N(6)-ACETYLLYSINE HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID FORMUL 2 ALY C8 H16 N2 O3 FORMUL 3 PEG 3(C4 H10 O3) FORMUL 6 MES C6 H13 N O4 S FORMUL 7 HOH *67(H2 O) HELIX 1 AA1 LEU A -2 VAL A 2 5 5 HELIX 2 AA2 GLU A 94 ALA A 96 5 3 HELIX 3 AA3 LYS A 124 ALA A 132 1 9 HELIX 4 AA4 LYS A 133 GLY A 135 5 3 SHEET 1 AA1 3 GLU A 45 PRO A 47 0 SHEET 2 AA1 3 ARG A 30 LEU A 39 -1 N LEU A 38 O ILE A 46 SHEET 3 AA1 3 ILE A 76 GLY A 80 -1 O GLY A 80 N ARG A 30 SHEET 1 AA2 4 GLU A 45 PRO A 47 0 SHEET 2 AA2 4 ARG A 30 LEU A 39 -1 N LEU A 38 O ILE A 46 SHEET 3 AA2 4 THR A 4 ILE A 17 -1 N HIS A 16 O GLN A 31 SHEET 4 AA2 4 SER A 111 PRO A 121 -1 O ILE A 120 N VAL A 5 SHEET 1 AA3 4 ASN A 66 PHE A 69 0 SHEET 2 AA3 4 PHE A 51 HIS A 57 -1 N VAL A 54 O PHE A 69 SHEET 3 AA3 4 PHE A 84 LEU A 92 -1 O SER A 89 N ILE A 55 SHEET 4 AA3 4 GLY A 97 LEU A 105 -1 O HIS A 103 N LEU A 86 LINK C ARG C 7 N ALY C 8 1555 1555 1.33 LINK C ALY C 8 N SER C 9 1555 1555 1.34 CISPEP 1 PRO A 72 PRO A 73 0 4.64 SITE 1 AC1 4 GLU A 20 LYS A 53 THR A 68 GLU A 129 SITE 1 AC2 2 LYS A 95 LYS A 133 SITE 1 AC3 4 GLU A 94 GLU A 98 LYS A 100 LYS A 124 SITE 1 AC4 1 TRP A 81 CRYST1 113.164 113.164 26.524 90.00 90.00 120.00 P 65 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 0.008837 0.005102 0.000000 0.00000 SCALE2 0.000000 0.010204 0.000000 0.00000 SCALE3 0.000000 0.000000 0.037702 0.00000