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- PDB-1qn7: Crystal structure of the T(-27) Adenovirus major late promoter TA... -

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Basic information

Entry
Database: PDB / ID: 1qn7
TitleCrystal structure of the T(-27) Adenovirus major late promoter TATA box variant bound to wild-type TBP (Arabidopsis thaliana TBP isoform 2). TATA element recognition by the TATA box-binding protein has been conserved throughout evolution.
Components
  • DNA (5'-D(*GP*CP*TP*AP*TP*AP*TP*AP*AP*GP*GP*GP*CP*A)-3')
  • DNA (5'-D(*TP*GP*CP*CP*CP*TP*TP*AP*TP*AP*TP*AP*GP*C)-3')
  • TRANSCRIPTION INITIATION FACTOR TFIID-1
KeywordsTATA BOX-BINDING PROTEIN (TBP) / ADENOVIRUS MAJOR LATE PROMOTER (ADMLP) TATA BOX / TBP-TATA ELEMENT COMPLEXES / T (- 27) TATA BOX VARIANT
Function / homology
Function and homology information


DNA-templated transcription initiation / DNA binding / nucleus
Similarity search - Function
TATA-Binding Protein / TATA-Binding Protein / TATA-box binding protein, eukaryotic / TATA-box binding protein / TATA-box binding protein, conserved site / Transcription factor TFIID (or TATA-binding protein, TBP) / Transcription factor TFIID repeat signature. / TBP domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / TATA-box-binding protein 1
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.3 Å
AuthorsPatikoglou, G.A. / Kim, J.L. / Sun, L. / Yang, S.-H. / Kodadek, T. / Burley, S.K.
CitationJournal: Genes Dev. / Year: 1999
Title: TATA Element Recognition by the TATA Box-Binding Protein Has Been Conserved Throughout Evolution
Authors: Patikoglou, G.A. / Kim, J.L. / Sun, L. / Yang, S.-H. / Kodadek, T. / Burley, S.K.
History
DepositionOct 14, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRANSCRIPTION INITIATION FACTOR TFIID-1
B: TRANSCRIPTION INITIATION FACTOR TFIID-1
C: DNA (5'-D(*GP*CP*TP*AP*TP*AP*TP*AP*AP*GP*GP*GP*CP*A)-3')
D: DNA (5'-D(*TP*GP*CP*CP*CP*TP*TP*AP*TP*AP*TP*AP*GP*C)-3')
E: DNA (5'-D(*GP*CP*TP*AP*TP*AP*TP*AP*AP*GP*GP*GP*CP*A)-3')
F: DNA (5'-D(*TP*GP*CP*CP*CP*TP*TP*AP*TP*AP*TP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)61,9206
Polymers61,9206
Non-polymers00
Water4,738263
1
A: TRANSCRIPTION INITIATION FACTOR TFIID-1
C: DNA (5'-D(*GP*CP*TP*AP*TP*AP*TP*AP*AP*GP*GP*GP*CP*A)-3')
D: DNA (5'-D(*TP*GP*CP*CP*CP*TP*TP*AP*TP*AP*TP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)30,9603
Polymers30,9603
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-9.2 kcal/mol
Surface area15170 Å2
MethodPQS
2
B: TRANSCRIPTION INITIATION FACTOR TFIID-1
E: DNA (5'-D(*GP*CP*TP*AP*TP*AP*TP*AP*AP*GP*GP*GP*CP*A)-3')
F: DNA (5'-D(*TP*GP*CP*CP*CP*TP*TP*AP*TP*AP*TP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)30,9603
Polymers30,9603
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-10.7 kcal/mol
Surface area14900 Å2
MethodPQS
Unit cell
Length a, b, c (Å)41.800, 146.700, 57.400
Angle α, β, γ (deg.)90.00, 90.50, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.99999, 0.00172, -0.00289), (0.00176, -0.99989, 0.01462), (-0.00287, -0.01463, -0.99989)
Vector: 8.99841, -88.3204, 217.52924)

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Components

#1: Protein TRANSCRIPTION INITIATION FACTOR TFIID-1 / TATA-BOX FACTOR 1 / TATA SEQUENCE-BINDING PROTEIN 1 / TBP1


Mass: 22400.354 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P28147
#2: DNA chain DNA (5'-D(*GP*CP*TP*AP*TP*AP*TP*AP*AP*GP*GP*GP*CP*A)-3')


Mass: 4328.841 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*TP*GP*CP*CP*CP*TP*TP*AP*TP*AP*TP*AP*GP*C)-3')


Mass: 4230.765 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O
Compound detailsDNA MOLECULES BOUND WITHIN THE SERIES CHAIN C, E CHAIN D, F 1QN3 GCTATAAACGGGCA TGCCCGTTTATAGC 1QN4 ...DNA MOLECULES BOUND WITHIN THE SERIES CHAIN C, E CHAIN D, F 1QN3 GCTATAAACGGGCA TGCCCGTTTATAGC 1QN4 GCTATAAAATGGCA TGCCATTTTATAGC 1QN5 GCTATAAGAGGGCA TGCCCTCTTATAGC 1QN6 GCTATAATAGGGCA TGCCCTATTATAGC 1QN7 GCTATATAAGGGCA TGCCCTTATATAGC 1QN8 GCTATTAAAGGGCA TGCCCTTTAATAGC 1QN9 GCTACAAAAGGGCA TGCCCTTTTGTAGC 1QNA GCTTTAAAAGGGCA TGCCCTTTTAAAGC 1QNB GCTATAAATGGGCA TGCCCATTTATAGC 1QNC GCAATAAAAGGGCA TGCCCTTTTATTGC 1QNE GCTATAAAAGGGCA TGCCCTTTTATAGC

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.72 %
Crystal growpH: 6 / Details: pH 6.00
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5.9 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.5 mMcomplex1drop
240 mMMES1drop
360 mM1dropor 100 mMKCl
44 mM1dropMgCl2
514 %(v/v)glycerol1drop
6300 mMammonium acetate1drop
710 mMdithiothreitol1drop
812 %(v/v)glycerol1reservoir
912 %(v/v)MES1reservoir
1010 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.92
DetectorDetector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.3→15 Å / Num. obs: 30019 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rsym value: 0.058
Reflection
*PLUS
Rmerge(I) obs: 0.058

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Processing

Software
NameClassification
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: OTHER / Resolution: 2.3→6 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.263 2481 10 %RANDOM
Rwork0.194 ---
obs0.194 27681 96.2 %-
Refinement stepCycle: LAST / Resolution: 2.3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2911 1134 0 263 4308
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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