HEADER TRANSCRIPTION 19-SEP-18 6MIP TITLE CRYSTAL STRUCTURE OF TAF14 YEATS DOMAIN G82A MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 14; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: YEATS DOMAIN RESIDUES 1-137; COMPND 5 SYNONYM: ACTIN NON-COMPLEMENTING MUTANT 1,CHROMOSOME STABILITY COMPND 6 PROTEIN 10,SWI/SNF CHROMATIN-REMODELING COMPLEX SUBUNIT TAF14,SWI/SNF COMPND 7 COMPLEX 29 KDA SUBUNIT,SWI/SNF COMPLEX SUBUNIT TAF14,TBP-ASSOCIATED COMPND 8 FACTOR 14,TBP-ASSOCIATED FACTOR 30 KDA,TRANSCRIPTION FACTOR G 30 KDA COMPND 9 SUBUNIT,TRANSCRIPTION INITIATION FACTOR TFIIF 30 KDA SUBUNIT; COMPND 10 ENGINEERED: YES; COMPND 11 MUTATION: 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 KEYWDS TRANSCRIPTION, EPIGENETIC, HISTONE READER EXPDTA X-RAY DIFFRACTION AUTHOR B.J.KLEIN,F.H.ANDREWS,T.G.KUTATELADZE REVDAT 2 11-OCT-23 6MIP 1 REMARK REVDAT 1 14-NOV-18 6MIP 0 JRNL AUTH B.J.KLEIN,K.R.VANN,F.H.ANDREWS,W.W.WANG,J.ZHANG,Y.ZHANG, JRNL AUTH 2 A.A.BELOGLAZKINA,W.MI,Y.LI,H.LI,X.SHI,A.G.KUTATELADZE, JRNL AUTH 3 B.D.STRAHL,W.R.LIU,T.G.KUTATELADZE JRNL TITL STRUCTURAL INSIGHTS INTO THE PI-PI-PI STACKING MECHANISM AND JRNL TITL 2 DNA-BINDING ACTIVITY OF THE YEATS DOMAIN. JRNL REF NAT COMMUN V. 9 4574 2018 JRNL REFN ESSN 2041-1723 JRNL PMID 30385749 JRNL DOI 10.1038/S41467-018-07072-6 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575) 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.11 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.9 REMARK 3 NUMBER OF REFLECTIONS : 12218 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 609 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 37.1134 - 3.1747 0.79 2607 135 0.1629 0.2076 REMARK 3 2 3.1747 - 2.5200 0.93 2958 157 0.2036 0.2254 REMARK 3 3 2.5200 - 2.2015 0.96 3035 157 0.1885 0.2347 REMARK 3 4 2.2015 - 2.0002 0.96 3009 160 0.1825 0.2210 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.940 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 : 0.007 1173 REMARK 3 ANGLE : 0.882 1598 REMARK 3 CHIRALITY : 0.060 179 REMARK 3 PLANARITY : 0.006 209 REMARK 3 DIHEDRAL : 12.952 713 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID -1 THROUGH 137) REMARK 3 ORIGIN FOR THE GROUP (A): -43.8938 13.2123 2.1980 REMARK 3 T TENSOR REMARK 3 T11: 0.2279 T22: 0.1810 REMARK 3 T33: 0.1494 T12: -0.0525 REMARK 3 T13: -0.0282 T23: 0.0443 REMARK 3 L TENSOR REMARK 3 L11: 1.1308 L22: 4.1882 REMARK 3 L33: 0.4845 L12: 1.3655 REMARK 3 L13: 0.1601 L23: 0.1898 REMARK 3 S TENSOR REMARK 3 S11: 0.1060 S12: -0.0651 S13: -0.0123 REMARK 3 S21: 0.1731 S22: -0.1942 S23: -0.4078 REMARK 3 S31: -0.1048 S32: 0.1909 S33: 0.0733 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 6MIP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-SEP-18. REMARK 100 THE DEPOSITION ID IS D_1000237002. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-APR-16 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) : 1.54 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 : 17536 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04200 REMARK 200 FOR THE DATA SET : 35.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.09200 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: 5IOK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 48% PEG600 WITH 0.2 M SODIUM CITRATE REMARK 280 (PH 6.0), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K 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 17.48133 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 8.74067 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 13.11100 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 4.37033 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 21.85167 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 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 GLY A -4 REMARK 465 PRO A -3 REMARK 465 LEU A -2 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 53.43 -95.58 REMARK 500 PRO A 23 151.78 -49.73 REMARK 500 ASN A 26 -1.73 76.60 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 DBREF 6MIP A 1 137 UNP P35189 TAF14_YEAST 1 137 SEQADV 6MIP GLY A -4 UNP P35189 EXPRESSION TAG SEQADV 6MIP PRO A -3 UNP P35189 EXPRESSION TAG SEQADV 6MIP LEU A -2 UNP P35189 EXPRESSION TAG SEQADV 6MIP GLY A -1 UNP P35189 EXPRESSION TAG SEQADV 6MIP SER A 0 UNP P35189 EXPRESSION TAG SEQADV 6MIP ALA A 82 UNP P35189 GLY 82 ENGINEERED MUTATION 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 ALA 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 HET PEG A 201 17 HETNAM PEG DI(HYDROXYETHYL)ETHER FORMUL 2 PEG C4 H10 O3 FORMUL 3 HOH *146(H2 O) HELIX 1 AA1 GLY A -1 VAL A 2 5 4 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 ILE A 46 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 ILE A 46 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 VAL A 54 O PHE A 69 SHEET 3 AA3 4 PRO A 85 LEU A 92 -1 O ASP A 87 N HIS A 57 SHEET 4 AA3 4 GLY A 97 ASP A 104 -1 O ARG A 99 N VAL A 90 CISPEP 1 PRO A 72 PRO A 73 0 2.92 SITE 1 AC1 6 VAL A 2 GLY A 83 ASN A 106 PHE A 107 SITE 2 AC1 6 HOH A 371 HOH A 393 CRYST1 113.364 113.364 26.222 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 0.008821 0.005093 0.000000 0.00000 SCALE2 0.000000 0.010186 0.000000 0.00000 SCALE3 0.000000 0.000000 0.038136 0.00000