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- PDB-6uep: Structure of A. thaliana TBP bound to a DNA site with a C-C mismatch -

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Basic information

Entry
Database: PDB / ID: 6uep
TitleStructure of A. thaliana TBP bound to a DNA site with a C-C mismatch
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*CP*TP*TP*TP*AP*TP*AP*GP*C)-3')
  • TATA-box-binding protein 1
KeywordsDNA BINDING PROTEIN/DNA / TBP / TATA / C-C mismatch / NER / 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
FORMIC ACID / 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: 2.05 Å
AuthorsSchumacher, M.A. / Al-hashimi, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM130290 United States
CitationJournal: Nature / Year: 2020
Title: DNA mismatches reveal conformational penalties in protein-DNA recognition.
Authors: Afek, A. / Shi, H. / Rangadurai, A. / Sahay, H. / Senitzki, A. / Xhani, S. / Fang, M. / Salinas, R. / Mielko, Z. / Pufall, M.A. / Poon, G.M.K. / Haran, T.E. / Schumacher, M.A. / Al-Hashimi, H.M. / Gordan, R.
History
DepositionSep 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_DOI / _citation.title
Revision 1.2Nov 4, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Mar 13, 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
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*CP*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*CP*TP*TP*TP*AP*TP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,39311
Polymers66,0706
Non-polymers3225
Water5,098283
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*CP*TP*TP*TP*AP*TP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1736
Polymers33,0353
Non-polymers1383
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-14 kcal/mol
Surface area13330 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*CP*TP*TP*TP*AP*TP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2195
Polymers33,0353
Non-polymers1842
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-18 kcal/mol
Surface area12640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.648, 46.654, 146.302
Angle α, β, γ (deg.)90.000, 95.510, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-317-

HOH

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Components

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Protein , 1 types, 2 molecules BA

#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: 24514.672 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

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DNA chain , 2 types, 4 molecules ECFD

#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*CP*TP*TP*TP*AP*TP*AP*GP*C)-3')


Mass: 4206.740 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 288 molecules

#4: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.92 Å3/Da / Density % sol: 57.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate pH 4.5 and 3.2 M sodium formate

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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 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→145.626 Å / Num. obs: 83131 / % possible obs: 93 % / Redundancy: 3 % / CC1/2: 0.998 / Rpim(I) all: 0.025 / Rsym value: 0.035 / Net I/σ(I): 18.4
Reflection shellResolution: 2.05→2.08 Å / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1725 / CC1/2: 0.838 / Rpim(I) all: 0.267 / Rsym value: 0.353

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→145.626 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.23 / Phase error: 21.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.192 3705 4.46 %
Rwork0.1715 79426 -
obs0.1724 83131 88.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.63 Å2 / Biso mean: 46.8402 Å2 / Biso min: 20.13 Å2
Refinement stepCycle: final / Resolution: 2.05→145.626 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2982 1130 21 283 4416
Biso mean--70.88 50.02 -
Num. residues----434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014323
X-RAY DIFFRACTIONf_angle_d1.046052
X-RAY DIFFRACTIONf_chiral_restr0.061686
X-RAY DIFFRACTIONf_plane_restr0.007569
X-RAY DIFFRACTIONf_dihedral_angle_d10.0642431
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.05-2.0770.2795790.2569172552
2.077-2.10540.26960.2577204958
2.1054-2.13550.25821050.2413216163
2.1355-2.16740.25091020.2395231768
2.1674-2.20130.25641270.2312265175
2.2013-2.23740.22381280.2279275381
2.2374-2.27590.24281450.2287314790
2.2759-2.31730.26521570.2217334897
2.3173-2.36190.21731550.2105341898
2.3619-2.41010.20691490.2081329298
2.4101-2.46250.24391640.2093340197
2.4625-2.51980.25041540.2122330897
2.5198-2.58280.24651540.2115333296
2.5828-2.65270.22971520.2082327094
2.6527-2.73070.22861500.2062330696
2.7307-2.81890.22171510.2115333897
2.8189-2.91970.24381620.2027340997
2.9197-3.03660.21831520.1974324196
3.0366-3.17480.20831560.1902318894
3.1748-3.34220.19691550.1766334294
3.3422-3.55160.18221540.159325196
3.5516-3.82580.16831520.143332595
3.8258-4.21090.20031440.14322794
4.2109-4.82020.11491560.1141322994
4.8202-6.0730.13741580.1389323193
6.073-145.6260.17951480.1619316792
Refinement TLS params.Method: refined / Origin x: -2.0979 Å / Origin y: 9.986 Å / Origin z: 41.1274 Å
111213212223313233
T0.2422 Å2-0.0169 Å20.0071 Å2-0.2036 Å2-0.0164 Å2--0.2303 Å2
L0.5224 °2-0.1734 °2-0.0123 °2-0.1804 °20.0544 °2--1.4776 °2
S0.0358 Å °0.0248 Å °-0.0042 Å °-0.0937 Å °-0.0504 Å °-0.0827 Å °-0.0714 Å °-0.2358 Å °-0.0078 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB10 - 200
2X-RAY DIFFRACTION1allE201 - 214
3X-RAY DIFFRACTION1allF215 - 228
4X-RAY DIFFRACTION1allA12 - 198
5X-RAY DIFFRACTION1allC201 - 214
6X-RAY DIFFRACTION1allD215 - 228
7X-RAY DIFFRACTION1allW131 - 531
8X-RAY DIFFRACTION1allH20
9X-RAY DIFFRACTION1allY20
10X-RAY DIFFRACTION1allS1 - 286

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