HEADER TRANSCRIPTION 08-MAR-16 5IOK TITLE CRYSTAL STRUCTURE OF TAF14 YEATS DOMAIN IN COMPLEX WITH HISTONE H3K9CR 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: (ACE)QTAR(KCR)ST; COMPND 12 CHAIN: C; COMPND 13 ENGINEERED: YES; COMPND 14 OTHER_DETAILS: THIS PEPTIDE IS N-TERMINALLY ACETYLATED 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 CROTONYLATION, CROTONYLLYSINE, EPIGENETICS, READER, HISTONE H3, KEYWDS 2 H3K9CR, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR F.H.ANDREWS,T.G.KUATELADZE REVDAT 6 15-NOV-23 5IOK 1 REMARK REVDAT 5 27-SEP-23 5IOK 1 REMARK REVDAT 4 23-AUG-17 5IOK 1 REMARK REVDAT 3 01-JUN-16 5IOK 1 JRNL REVDAT 2 04-MAY-16 5IOK 1 JRNL REVDAT 1 20-APR-16 5IOK 0 JRNL AUTH F.H.ANDREWS,S.A.SHINSKY,E.K.SHANLE,J.B.BRIDGERS,A.GEST, JRNL AUTH 2 I.K.TSUN,K.KRAJEWSKI,X.SHI,B.D.STRAHL,T.G.KUTATELADZE JRNL TITL THE TAF14 YEATS DOMAIN IS A READER OF HISTONE CROTONYLATION. JRNL REF NAT.CHEM.BIOL. V. 12 396 2016 JRNL REFN ESSN 1552-4469 JRNL PMID 27089029 JRNL DOI 10.1038/NCHEMBIO.2065 REMARK 2 REMARK 2 RESOLUTION. 2.22 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 2.22 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.65 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 9546 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 478 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 32.6512 - 3.2014 1.00 3177 167 0.1710 0.1924 REMARK 3 2 3.2014 - 2.5414 0.99 3072 160 0.2734 0.3053 REMARK 3 3 2.5414 - 2.2202 0.93 2819 151 0.2767 0.3422 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) : 30.420 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 1286 REMARK 3 ANGLE : 1.230 1749 REMARK 3 CHIRALITY : 0.042 192 REMARK 3 PLANARITY : 0.006 230 REMARK 3 DIHEDRAL : 14.391 488 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): 43.6113 13.0749 2.0210 REMARK 3 T TENSOR REMARK 3 T11: 0.1970 T22: 0.1684 REMARK 3 T33: 0.2242 T12: 0.0570 REMARK 3 T13: -0.0071 T23: -0.0443 REMARK 3 L TENSOR REMARK 3 L11: 2.2747 L22: 5.2768 REMARK 3 L33: 0.9508 L12: -2.0209 REMARK 3 L13: 0.4079 L23: -0.5672 REMARK 3 S TENSOR REMARK 3 S11: 0.0825 S12: 0.0767 S13: 0.0728 REMARK 3 S21: -0.1244 S22: -0.1344 S23: 0.1835 REMARK 3 S31: -0.0694 S32: -0.1313 S33: 0.0363 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 5IOK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000219159. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 200K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9584 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.220 REMARK 200 RESOLUTION RANGE LOW (A) : 32.650 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : 0.08000 REMARK 200 FOR THE DATA SET : 24.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.22 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 72.6 REMARK 200 DATA REDUNDANCY IN SHELL : 1.40 REMARK 200 R MERGE FOR SHELL (I) : 0.33000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 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: 5D7E REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 44% PEG600 (V/V) AND 0.2 M CITRIC ACID REMARK 280 (PH 6.0), 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 17.45067 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 8.72533 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 13.08800 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 4.36267 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 21.81333 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: 1400 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 1.0 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 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 301 O HOH A 399 2.04 REMARK 500 O HOH A 356 O HOH A 391 2.16 REMARK 500 O HOH A 346 O HOH A 397 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 ASN A 26 -5.02 72.82 REMARK 500 LEU A 93 156.56 -49.96 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 DBREF 5IOK A 1 137 UNP P35189 TAF14_YEAST 1 137 DBREF 5IOK C 3 10 PDB 5IOK 5IOK 3 10 SEQADV 5IOK GLY A -4 UNP P35189 EXPRESSION TAG SEQADV 5IOK PRO A -3 UNP P35189 EXPRESSION TAG SEQADV 5IOK LEU A -2 UNP P35189 EXPRESSION TAG SEQADV 5IOK GLY A -1 UNP P35189 EXPRESSION TAG SEQADV 5IOK SER A 0 UNP P35189 EXPRESSION TAG SEQRES 1 A 142 GLY PRO LEU GLY SER MET VAL ALA THR VAL LYS ARG THR SEQRES 2 A 142 ILE ARG ILE LYS THR GLN GLN HIS ILE LEU PRO GLU VAL SEQRES 3 A 142 PRO PRO VAL GLU ASN PHE PRO VAL ARG GLN TRP SER ILE SEQRES 4 A 142 GLU ILE VAL LEU LEU ASP ASP GLU GLY LYS GLU ILE PRO SEQRES 5 A 142 ALA THR ILE PHE ASP LYS VAL ILE TYR HIS LEU HIS PRO SEQRES 6 A 142 THR PHE ALA ASN PRO ASN ARG THR PHE THR ASP PRO PRO SEQRES 7 A 142 PHE ARG ILE GLU GLU GLN GLY TRP GLY GLY PHE PRO LEU SEQRES 8 A 142 ASP ILE SER VAL PHE LEU LEU GLU LYS ALA GLY GLU ARG SEQRES 9 A 142 LYS ILE PRO HIS ASP LEU ASN PHE LEU GLN GLU SER TYR SEQRES 10 A 142 GLU VAL GLU HIS VAL ILE GLN ILE PRO LEU ASN LYS PRO SEQRES 11 A 142 LEU LEU THR GLU GLU LEU ALA LYS SER GLY SER THR SEQRES 1 C 8 ACE GLN THR ALA ARG KCR SER THR HET ACE C 3 3 HET KCR C 8 14 HET PEG A 201 7 HET PEG A 202 7 HETNAM ACE ACETYL GROUP HETNAM KCR N-6-CROTONYL-L-LYSINE HETNAM PEG DI(HYDROXYETHYL)ETHER FORMUL 2 ACE C2 H4 O FORMUL 2 KCR C10 H18 N2 O3 FORMUL 3 PEG 2(C4 H10 O3) FORMUL 5 HOH *113(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 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 LYS A 12 O GLU A 35 SHEET 4 AA2 4 SER A 111 PRO A 121 -1 O VAL A 114 N ILE A 11 SHEET 1 AA3 4 ASN A 66 PHE A 69 0 SHEET 2 AA3 4 PHE A 51 HIS A 57 -1 N TYR A 56 O ARG A 67 SHEET 3 AA3 4 PHE A 84 LEU A 92 -1 O SER A 89 N ILE A 55 SHEET 4 AA3 4 GLU A 98 LEU A 105 -1 O HIS A 103 N LEU A 86 LINK C ACE C 3 N GLN C 4 1555 1555 1.33 LINK C ARG C 7 N KCR C 8 1555 1555 1.33 LINK C KCR C 8 N SER C 9 1555 1555 1.33 CISPEP 1 PRO A 72 PRO A 73 0 1.98 SITE 1 AC1 7 SER A 0 GLU A 20 LYS A 53 THR A 68 SITE 2 AC1 7 PHE A 91 GLU A 129 HOH A 302 SITE 1 AC2 5 MET A 1 LYS A 95 ARG A 99 GLN A 119 SITE 2 AC2 5 HOH A 361 CRYST1 113.095 113.095 26.176 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 0.008842 0.005105 0.000000 0.00000 SCALE2 0.000000 0.010210 0.000000 0.00000 SCALE3 0.000000 0.000000 0.038203 0.00000