HEADER TRANSCRIPTION 29-JUN-12 4B0A TITLE THE HIGH-RESOLUTION STRUCTURE OF YTBP-YTAF1 IDENTIFIES CONSERVED AND TITLE 2 COMPETING INTERACTION SURFACES IN TRANSCRIPTIONAL ACTIVATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 1, LINKER, COMPND 3 TATA-BOX-BINDING PROTEIN; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: TAF1 RESIDUES 8-71, LINKER, TBP RESIDUE 61-240; COMPND 6 SYNONYM: TATA SEQUENCE-BINDING PROTEIN, TBP, TATA-BINDING FACTOR, COMPND 7 TATA-BOX FACTOR, TRANSCRIPTION FACTOR D, TRANSCRIPTION INITIATION COMPND 8 FACTOR TFIID TBP SUBUNIT, TAFII-130, TAFII-145, TBP-ASSOCIATED FACTOR COMPND 9 1, TBP-ASSOCIATED FACTOR 145 KDA; COMPND 10 EC: 2.3.1.48; COMPND 11 ENGINEERED: YES; COMPND 12 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_TAXID: 4932; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET28B KEYWDS TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR M.ANANDAPADAMANABAN,C.ANDRESEN,M.SIPONEN,T.KOKUBO,M.IKURA,M.MOCHE, AUTHOR 2 M.SUNNERHAGEN REVDAT 5 20-DEC-23 4B0A 1 REMARK LINK REVDAT 4 21-AUG-13 4B0A 1 JRNL REVDAT 3 24-JUL-13 4B0A 1 JRNL REVDAT 2 17-JUL-13 4B0A 1 JRNL REVDAT 1 03-JUL-13 4B0A 0 JRNL AUTH M.ANANDAPADAMANABAN,C.ANDRESEN,M.SIPONEN,T.KOKUBO,M.IKURA, JRNL AUTH 2 M.MOCHE,M.SUNNERHAGEN JRNL TITL HIGH-RESOLUTION STRUCTURE OF TBP WITH TAF1 REVEALS ANCHORING JRNL TITL 2 PATTERNS IN TRANSCRIPTIONAL REGULATION JRNL REF NAT.STRUCT.MOL.BIOL. V. 20 1008 2013 JRNL REFN ISSN 1545-9993 JRNL PMID 23851461 JRNL DOI 10.1038/NSMB.2611 REMARK 2 REMARK 2 RESOLUTION. 1.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.1 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 59.54 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 17873 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 888 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 9 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.97 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.09 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.36 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2805 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.1868 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2678 REMARK 3 BIN R VALUE (WORKING SET) : 0.1851 REMARK 3 BIN FREE R VALUE : 0.2210 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.53 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 127 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1851 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 213 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.64 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.39 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.27270 REMARK 3 B22 (A**2) : 2.58900 REMARK 3 B33 (A**2) : 0.68360 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.180 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.176 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.160 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.159 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.154 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.919 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 2008 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 2710 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 949 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 49 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 295 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 2008 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 2 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 262 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 2561 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.02 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.50 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 2.63 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT NOTE 1: IDEAL-DIST CONTACT REMARK 3 SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CL CA REMARK 3 GOL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=2149. NUMBER REMARK 3 WITH APPROX DEFAULT CCP4 ATOM TYPE=37. NUMBER TREATED BY BAD NON- REMARK 3 BONDED CONTACTS=3. REMARK 4 REMARK 4 4B0A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-JUN-12. REMARK 100 THE DEPOSITION ID IS D_1290052931. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUL-11 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 : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9334 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17942 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.970 REMARK 200 RESOLUTION RANGE LOW (A) : 59.540 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 0.58000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1YTB REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 16.44700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.83350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.12650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.83350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.44700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.12650 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 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 MET A -13 REMARK 465 GLY A -12 REMARK 465 SER A -11 REMARK 465 SER A -10 REMARK 465 HIS A -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 SER A -3 REMARK 465 SER A -2 REMARK 465 GLY A -1 REMARK 465 LEU A 0 REMARK 465 VAL A 1 REMARK 465 PRO A 2 REMARK 465 ARG A 3 REMARK 465 GLY A 4 REMARK 465 SER A 5 REMARK 465 HIS A 6 REMARK 465 MET A 7 REMARK 465 GLY A 8 REMARK 465 ASP A 67 REMARK 465 ASP A 68 REMARK 465 ASP A 69 REMARK 465 LEU A 70 REMARK 465 PRO A 71 REMARK 465 GLY A 72 REMARK 465 GLY A 73 REMARK 465 GLY A 74 REMARK 465 SER A 75 REMARK 465 GLY A 76 REMARK 465 GLY A 77 REMARK 465 GLY A 78 REMARK 465 SER A 79 REMARK 465 GLY A 80 REMARK 465 GLY A 81 REMARK 465 GLY A 82 REMARK 465 SER A 83 REMARK 465 MET A 84 REMARK 465 SER A 161 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 A 45 CG CD CE NZ REMARK 470 LYS A 299 CG CD CE NZ 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 2121 O HOH A 2123 2.13 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 HIS A 279 44.54 -108.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1067 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 37 O REMARK 620 2 ASP A 39 O 90.0 REMARK 620 3 ASP A 39 O 94.7 8.3 REMARK 620 4 GLU A 288 OE2 87.2 173.6 167.3 REMARK 620 5 HOH A2041 O 73.7 79.0 86.9 105.7 REMARK 620 6 HOH A2042 O 86.6 85.9 79.3 88.2 155.0 REMARK 620 7 HOH A2045 O 147.3 69.6 62.5 110.2 123.8 67.3 REMARK 620 8 HOH A2081 O 133.9 101.0 102.4 85.0 65.0 138.3 76.7 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1068 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 39 OD1 REMARK 620 2 ASP A 46 OD1 100.3 REMARK 620 3 ASN A 195 OD1 77.7 85.3 REMARK 620 4 HOH A2046 O 92.4 167.2 95.9 REMARK 620 5 HOH A2053 O 139.9 91.9 141.7 79.2 REMARK 620 6 HOH A2054 O 147.9 71.3 70.8 97.1 72.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1244 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 280 O REMARK 620 2 SER A 283 O 85.0 REMARK 620 3 SER A 283 O 81.5 14.4 REMARK 620 4 HOH A2163 O 84.3 88.0 73.8 REMARK 620 5 HOH A2166 O 73.4 152.8 140.6 73.9 REMARK 620 6 HOH A2167 O 80.5 73.8 87.0 157.1 117.3 REMARK 620 7 HOH A2168 O 85.7 135.5 147.9 134.1 60.3 61.8 REMARK 620 8 HOH A2172 O 161.1 100.4 99.3 77.9 95.4 118.4 102.2 REMARK 620 9 HOH A2173 O 138.0 84.6 96.5 135.7 122.5 57.6 74.0 60.9 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1067 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1068 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1069 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1070 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1071 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1241 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1242 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1243 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1244 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1245 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NGM RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A YEAST BRF1-TBP-DNA TERNARY COMPLEX REMARK 900 RELATED ID: 1NH2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A YEAST TFIIA/TBP/DNA COMPLEX REMARK 900 RELATED ID: 1RM1 RELATED DB: PDB REMARK 900 STRUCTURE OF A YEAST TFIIA/TBP/TATA-BOX DNA COMPLEX REMARK 900 RELATED ID: 1TBA RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF A TBP-TAFII230 COMPLEX: PROTEINMIMICRY OF THE REMARK 900 MINOR GROOVE SURFACE OF THE TATA BOX UNWOUNDBY TBP, NMR, 25 REMARK 900 STRUCTURES REMARK 900 RELATED ID: 1TBP RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF YEAST TATA-BINDING PROTEIN AND MODEL FOR REMARK 900 INTERACTION WITH DNA REMARK 900 RELATED ID: 1YTB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A YEAST TBP/TATA-BOX COMPLEX REMARK 900 RELATED ID: 1YTF RELATED DB: PDB REMARK 900 YEAST TFIIA/TBP/DNA COMPLEX YEAST TFIIA/TBP/DEOXYRIBONUCLEIC ACID REMARK 900 COMPLEX REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE ENTRY CONTAINS AN ENGINEERED FUSION PROTEIN. REMARK 999 THE TAND1 AND TAND2 REGION (8-71) OF TAF1 IS COVALENTLY REMARK 999 LINKED VIA A PROTEIN LINKER (GGGSGGGSGGGS) TO TBP (61-240) REMARK 999 IN ORDER TO ACCOMMODATE THESE IN THE SAME PDB CHAIN AN REMARK 999 OFFSET OF 100 HAS BEEN APPLIED TO THE TBP RESIDUE NUMBERING REMARK 999 AND SO THIS NOW RUNS FROM 161 TO 340 RATHER THAN 61 TO 240. REMARK 999 OTHER_DETAILS: CONSTRUCTS CONTAIN RESIDUE: 8-71 MUTATIONS: REMARK 999 G41A AND A42R, WHICH ARE DUE TO A CLONING ARTIFACT, RELATIVE TO REMARK 999 THE UNIPROT ENTRY: P46677 DBREF 4B0A A 8 71 UNP P46677 TAF1_YEAST 8 71 DBREF 4B0A A 161 340 UNP P13393 TBP_YEAST 61 240 SEQADV 4B0A MET A -13 UNP P46677 EXPRESSION TAG SEQADV 4B0A GLY A -12 UNP P46677 EXPRESSION TAG SEQADV 4B0A SER A -11 UNP P46677 EXPRESSION TAG SEQADV 4B0A SER A -10 UNP P46677 EXPRESSION TAG SEQADV 4B0A HIS A -9 UNP P46677 EXPRESSION TAG SEQADV 4B0A HIS A -8 UNP P46677 EXPRESSION TAG SEQADV 4B0A HIS A -7 UNP P46677 EXPRESSION TAG SEQADV 4B0A HIS A -6 UNP P46677 EXPRESSION TAG SEQADV 4B0A HIS A -5 UNP P46677 EXPRESSION TAG SEQADV 4B0A HIS A -4 UNP P46677 EXPRESSION TAG SEQADV 4B0A SER A -3 UNP P46677 EXPRESSION TAG SEQADV 4B0A SER A -2 UNP P46677 EXPRESSION TAG SEQADV 4B0A GLY A -1 UNP P46677 EXPRESSION TAG SEQADV 4B0A LEU A 0 UNP P46677 EXPRESSION TAG SEQADV 4B0A VAL A 1 UNP P46677 EXPRESSION TAG SEQADV 4B0A PRO A 2 UNP P46677 EXPRESSION TAG SEQADV 4B0A ARG A 3 UNP P46677 EXPRESSION TAG SEQADV 4B0A GLY A 4 UNP P46677 EXPRESSION TAG SEQADV 4B0A SER A 5 UNP P46677 EXPRESSION TAG SEQADV 4B0A HIS A 6 UNP P46677 EXPRESSION TAG SEQADV 4B0A MET A 7 UNP P46677 EXPRESSION TAG SEQADV 4B0A ALA A 41 UNP P13393 GLY 41 ENGINEERED MUTATION SEQADV 4B0A ARG A 42 UNP P13393 ALA 42 ENGINEERED MUTATION SEQADV 4B0A GLY A 72 UNP P46677 LINKER SEQADV 4B0A GLY A 73 UNP P46677 LINKER SEQADV 4B0A GLY A 74 UNP P46677 LINKER SEQADV 4B0A SER A 75 UNP P46677 LINKER SEQADV 4B0A GLY A 76 UNP P46677 LINKER SEQADV 4B0A GLY A 77 UNP P46677 LINKER SEQADV 4B0A GLY A 78 UNP P46677 LINKER SEQADV 4B0A SER A 79 UNP P46677 LINKER SEQADV 4B0A GLY A 80 UNP P46677 LINKER SEQADV 4B0A GLY A 81 UNP P46677 LINKER SEQADV 4B0A GLY A 82 UNP P46677 LINKER SEQADV 4B0A SER A 83 UNP P46677 LINKER SEQADV 4B0A MET A 84 UNP P46677 LINKER SEQRES 1 A 278 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 278 LEU VAL PRO ARG GLY SER HIS MET GLY LYS THR ASN LEU SEQRES 3 A 278 ALA ASN GLU ASP GLU ALA TYR GLU ALA ILE PHE GLY GLY SEQRES 4 A 278 GLU PHE GLY SER LEU GLU ILE GLY SER TYR ILE GLY GLY SEQRES 5 A 278 ASP GLU ALA ARG ASN SER LYS ASP TYR THR GLU HIS LEU SEQRES 6 A 278 PRO ASP ALA VAL ASP PHE GLU ASP GLU ASP GLU LEU ALA SEQRES 7 A 278 ASP ASP ASP ASP ASP LEU PRO GLY GLY GLY SER GLY GLY SEQRES 8 A 278 GLY SER GLY GLY GLY SER MET SER GLY ILE VAL PRO THR SEQRES 9 A 278 LEU GLN ASN ILE VAL ALA THR VAL THR LEU GLY CYS ARG SEQRES 10 A 278 LEU ASP LEU LYS THR VAL ALA LEU HIS ALA ARG ASN ALA SEQRES 11 A 278 GLU TYR ASN PRO LYS ARG PHE ALA ALA VAL ILE MET ARG SEQRES 12 A 278 ILE ARG GLU PRO LYS THR THR ALA LEU ILE PHE ALA SER SEQRES 13 A 278 GLY LYS MET VAL VAL THR GLY ALA LYS SER GLU ASP ASP SEQRES 14 A 278 SER LYS LEU ALA SER ARG LYS TYR ALA ARG ILE ILE GLN SEQRES 15 A 278 LYS ILE GLY PHE ALA ALA LYS PHE THR ASP PHE LYS ILE SEQRES 16 A 278 GLN ASN ILE VAL GLY SER CYS ASP VAL LYS PHE PRO ILE SEQRES 17 A 278 ARG LEU GLU GLY LEU ALA PHE SER HIS GLY THR PHE SER SEQRES 18 A 278 SER TYR GLU PRO GLU LEU PHE PRO GLY LEU ILE TYR ARG SEQRES 19 A 278 MET VAL LYS PRO LYS ILE VAL LEU LEU ILE PHE VAL SER SEQRES 20 A 278 GLY LYS ILE VAL LEU THR GLY ALA LYS GLN ARG GLU GLU SEQRES 21 A 278 ILE TYR GLN ALA PHE GLU ALA ILE TYR PRO VAL LEU SER SEQRES 22 A 278 GLU PHE ARG LYS MET HET CA A1067 1 HET CA A1068 1 HET GOL A1069 6 HET GOL A1070 6 HET GOL A1071 6 HET GOL A1241 6 HET GOL A1242 6 HET GOL A1243 6 HET CA A1244 1 HET CL A1245 1 HETNAM CA CALCIUM ION HETNAM GOL GLYCEROL HETNAM CL CHLORIDE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 CA 3(CA 2+) FORMUL 4 GOL 6(C3 H8 O3) FORMUL 11 CL CL 1- FORMUL 12 HOH *213(H2 O) HELIX 1 1 ASN A 14 GLY A 24 1 11 HELIX 2 2 PHE A 27 ILE A 36 5 10 HELIX 3 3 ASP A 181 ALA A 189 1 9 HELIX 4 4 SER A 228 GLY A 247 1 20 HELIX 5 5 ARG A 271 HIS A 279 1 9 HELIX 6 6 GLN A 319 PHE A 337 1 19 SHEET 1 AA10 ALA A 192 TYR A 194 0 SHEET 2 AA10 VAL A 202 ILE A 206 -1 O ILE A 203 N GLU A 193 SHEET 3 AA10 THR A 211 ILE A 215 -1 O THR A 211 N ILE A 206 SHEET 4 AA10 LYS A 220 ALA A 226 -1 O VAL A 222 N LEU A 214 SHEET 5 AA10 THR A 166 THR A 175 -1 O ILE A 170 N ALA A 226 SHEET 6 AA10 THR A 253 ASP A 265 -1 O THR A 253 N THR A 175 SHEET 7 AA10 LYS A 311 ALA A 317 -1 O ILE A 312 N CYS A 264 SHEET 8 AA10 VAL A 303 ILE A 306 -1 O VAL A 303 N THR A 315 SHEET 9 AA10 LEU A 293 ARG A 296 -1 O LEU A 293 N ILE A 306 SHEET 10 AA10 SER A 283 SER A 284 -1 O SER A 284 N ILE A 294 LINK O GLY A 37 CA CA A1067 1555 1555 2.12 LINK O AASP A 39 CA CA A1067 1555 1555 2.57 LINK O BASP A 39 CA CA A1067 1555 1555 2.95 LINK OD1AASP A 39 CA CA A1068 1555 1555 2.39 LINK OD1 ASP A 46 CA CA A1068 1555 1555 2.36 LINK OD1 ASN A 195 CA CA A1068 1555 1555 2.55 LINK O GLY A 280 CA CA A1244 1555 1555 2.34 LINK O ASER A 283 CA CA A1244 1555 1555 2.42 LINK O BSER A 283 CA CA A1244 1555 1555 2.44 LINK OE2 GLU A 288 CA CA A1067 4465 1555 2.74 LINK CA CA A1067 O HOH A2041 1555 1555 2.38 LINK CA CA A1067 O HOH A2042 1555 1555 2.51 LINK CA CA A1067 O HOH A2045 1555 1555 2.60 LINK CA CA A1067 O HOH A2081 1555 1555 2.63 LINK CA CA A1068 O HOH A2046 1555 1555 2.02 LINK CA CA A1068 O HOH A2053 1555 1555 2.70 LINK CA CA A1068 O HOH A2054 1555 1555 2.53 LINK CA CA A1244 O HOH A2163 1555 1555 2.28 LINK CA CA A1244 O HOH A2166 1555 1555 2.54 LINK CA CA A1244 O HOH A2167 1555 1555 2.43 LINK CA CA A1244 O HOH A2168 1555 1555 2.72 LINK CA CA A1244 O HOH A2172 1555 1555 2.19 LINK CA CA A1244 O HOH A2173 1555 1555 2.84 CISPEP 1 GLU A 208 PRO A 209 0 -7.28 CISPEP 2 LYS A 299 PRO A 300 0 -6.74 SITE 1 AC1 7 GLY A 37 ASP A 39 GLU A 288 HOH A2041 SITE 2 AC1 7 HOH A2042 HOH A2045 HOH A2081 SITE 1 AC2 6 ASP A 39 ASP A 46 ASN A 195 HOH A2046 SITE 2 AC2 6 HOH A2053 HOH A2054 SITE 1 AC3 8 ASP A 16 TYR A 19 GLU A 20 GLU A 49 SITE 2 AC3 8 HIS A 50 ARG A 190 LYS A 220 HOH A2015 SITE 1 AC4 6 TYR A 19 PHE A 23 ARG A 190 GLN A 258 SITE 2 AC4 6 HOH A2065 HOH A2066 SITE 1 AC5 9 GLU A 20 ASP A 39 GLU A 40 ALA A 41 SITE 2 AC5 9 ASP A 46 TYR A 47 HOH A2047 HOH A2049 SITE 3 AC5 9 HOH A2055 SITE 1 AC6 7 GLU A 26 PHE A 27 ARG A 296 LYS A 301 SITE 2 AC6 7 VAL A 303 GLY A 316 HOH A2027 SITE 1 AC7 10 ILE A 36 LYS A 210 THR A 211 THR A 212 SITE 2 AC7 10 GLY A 225 GOL A1243 HOH A2126 HOH A2133 SITE 3 AC7 10 HOH A2208 HOH A2210 SITE 1 AC8 10 ILE A 32 GLY A 33 ILE A 36 ASN A 169 SITE 2 AC8 10 THR A 224 GLY A 225 GOL A1242 HOH A2033 SITE 3 AC8 10 HOH A2211 HOH A2212 SITE 1 AC9 9 GLU A 31 GLY A 280 SER A 283 HOH A2163 SITE 2 AC9 9 HOH A2166 HOH A2167 HOH A2168 HOH A2172 SITE 3 AC9 9 HOH A2173 SITE 1 BC1 3 LEU A 12 ARG A 271 GLY A 274 CRYST1 32.894 74.253 99.667 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 0.030401 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013467 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010033 0.00000