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- PDB-6njq: Structure of TBP-Hoogsteen containing DNA complex -

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Basic information

Entry
Database: PDB / ID: 6njq
TitleStructure of TBP-Hoogsteen containing DNA complex
Components
  • DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*CP*GP*GP*GP*CP*A)-3')
  • DNA (5'-D(*TP*GP*CP*CP*CP*GP*TP*TP*TP*AP*TP*AP*GP*C)-3')
  • TATA-box-binding protein 1
KeywordsDNA BINDING PROTEIN/DNA / TBP / Hoogsteen / protein-DNA / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


DNA-templated transcription initiation / DNA binding / nucleus
Similarity search - Function
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
Similarity search - Domain/homology
DNA / DNA (> 10) / TATA-box-binding protein 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 Å
AuthorsSchumacher, M.A. / Stelling, A.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2019
Title: Infrared Spectroscopic Observation of a G-C+Hoogsteen Base Pair in the DNA:TATA-Box Binding Protein Complex Under Solution Conditions.
Authors: Stelling, A.L. / Liu, A.Y. / Zeng, W. / Salinas, R. / Schumacher, M.A. / Al-Hashimi, H.M.
History
DepositionJan 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: TATA-box-binding protein 1
E: DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*CP*GP*GP*GP*CP*A)-3')
F: DNA (5'-D(*TP*GP*CP*CP*CP*GP*TP*TP*TP*AP*TP*AP*GP*C)-3')
A: TATA-box-binding protein 1
C: DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*CP*GP*GP*GP*CP*A)-3')
D: DNA (5'-D(*TP*GP*CP*CP*CP*GP*TP*TP*TP*AP*TP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)66,2656
Polymers66,2656
Non-polymers00
Water61334
1
B: TATA-box-binding protein 1
E: DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*CP*GP*GP*GP*CP*A)-3')
F: DNA (5'-D(*TP*GP*CP*CP*CP*GP*TP*TP*TP*AP*TP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)33,1323
Polymers33,1323
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-20 kcal/mol
Surface area12900 Å2
MethodPISA
2
A: TATA-box-binding protein 1
C: DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*CP*GP*GP*GP*CP*A)-3')
D: DNA (5'-D(*TP*GP*CP*CP*CP*GP*TP*TP*TP*AP*TP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)33,1323
Polymers33,1323
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-17 kcal/mol
Surface area12780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.299, 57.967, 149.752
Angle α, β, γ (deg.)90.000, 96.500, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TATA-box-binding protein 1 / AtTBP1 / TATA sequence-binding protein 1 / TBP-1 / TATA-binding factor 1 / TATA-box factor 1 / ...AtTBP1 / TATA sequence-binding protein 1 / TBP-1 / TATA-binding factor 1 / TATA-box factor 1 / Transcription initiation factor TFIID TBP-1 subunit


Mass: 24571.725 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TBP1, At3g13445, MRP15.10 / Production host: Escherichia coli (E. coli) / References: UniProt: P28147
#2: DNA chain DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*CP*GP*GP*GP*CP*A)-3')


Mass: 4313.831 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*GP*CP*CP*CP*GP*TP*TP*TP*AP*TP*AP*GP*C)-3')


Mass: 4246.764 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

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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: 2.69 Å3/Da / Density % sol: 54.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 40 mM MES, 100 mM KCl, 4 mM MgCl2, 14% glycerol, 300 mM ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.01 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.01 Å / Relative weight: 1
ReflectionResolution: 2.75→148.79 Å / Num. obs: 18008 / % possible obs: 96.5 % / Redundancy: 3 % / Biso Wilson estimate: 50.56 Å2 / CC1/2: 0.97 / Rpim(I) all: 0.074 / Rsym value: 0.163 / Net I/σ(I): 7.3
Reflection shellResolution: 2.75→2.9 Å / Num. unique obs: 2622 / CC1/2: 0.824 / Rpim(I) all: 0.244 / Rsym value: 0.545

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QN3

1qn3


Resolution: 2.75→148.789 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 29.69
RfactorNum. reflection% reflection
Rfree0.2777 1810 10.05 %
Rwork0.23 --
obs0.2348 18008 97.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 238.32 Å2 / Biso mean: 52.0422 Å2 / Biso min: 7.9 Å2
Refinement stepCycle: final / Resolution: 2.75→148.789 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2942 1136 0 34 4112
Biso mean---37.81 -
Num. residues----430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044274
X-RAY DIFFRACTIONf_angle_d0.7155999
X-RAY DIFFRACTIONf_chiral_restr0.047682
X-RAY DIFFRACTIONf_plane_restr0.005561
X-RAY DIFFRACTIONf_dihedral_angle_d15.82397
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7501-2.82440.36351320.29891230136299
2.8244-2.90750.33831420.28461256139898
2.9075-3.00140.32081430.28461250139399
3.0014-3.10870.36581410.27741254139598
3.1087-3.23310.29281450.25241251139697
3.2331-3.38030.31791380.23641271140999
3.3803-3.55850.29151450.23851233137898
3.5585-3.78150.4041140.35121106122085
3.7815-4.07350.2981360.22961234137097
4.0735-4.48340.24591430.18341270141398
4.4834-5.13220.21871400.17451264140497
5.1322-6.46610.20511420.18941272141498
6.4661-149.00750.21861490.1891307145697
Refinement TLS params.Method: refined / Origin x: 2.0175 Å / Origin y: -3.1037 Å / Origin z: 37.2296 Å
111213212223313233
T0.0421 Å2-0.0026 Å2-0.0033 Å2-0.0788 Å20.0028 Å2--0.1084 Å2
L-0.12 °20.0619 °2-0.1042 °2-0.1811 °2-0.2952 °2--2.0094 °2
S0.0501 Å °0.0248 Å °0.0034 Å °0.0085 Å °0.0153 Å °-0.0259 Å °-0.0229 Å °0.0635 Å °0.0647 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB12 - 198
2X-RAY DIFFRACTION1allE201 - 214
3X-RAY DIFFRACTION1allF215 - 228
4X-RAY DIFFRACTION1allA12 - 198
5X-RAY DIFFRACTION1allC201 - 214
6X-RAY DIFFRACTION1allD215 - 228
7X-RAY DIFFRACTION1allT1 - 34

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