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- PDB-7vp2: Structure of a transcription factor and DNA complex -

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Basic information

Entry
Database: PDB / ID: 7vp2
TitleStructure of a transcription factor and DNA complex
Components
  • DNA (5'-D(*AP*TP*GP*TP*GP*GP*TP*CP*CP*CP*CP*AP*CP*T)-3')
  • DNA (5'-D(*TP*AP*GP*TP*GP*GP*GP*GP*AP*CP*CP*AP*CP*A)-3')
  • Transcription factor TCP10
KeywordsDNA BINDING PROTEIN / Complex / Transcription factor / TRANSCRIPTION / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


leaf senescence / leaf development / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding / nucleus
Similarity search - Function
Transcription factor, TCP / Transcription factor TCP subgroup / TCP family transcription factor / TCP domain profile.
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcription factor TCP10
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsZhang, Y. / Xu, Y.P. / Wang, B. / Su, X.D.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31670740 China
National Science Foundation (NSF, China)31270803 China
CitationJournal: To Be Published
Title: Structural basis for DNA recognition by TCP transcription factors
Authors: Zhang, Y. / Xu, Y.P. / Wang, B. / Su, X.D.
History
DepositionOct 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Transcription factor TCP10
A: Transcription factor TCP10
C: DNA (5'-D(*AP*TP*GP*TP*GP*GP*TP*CP*CP*CP*CP*AP*CP*T)-3')
D: DNA (5'-D(*TP*AP*GP*TP*GP*GP*GP*GP*AP*CP*CP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)32,3354
Polymers32,3354
Non-polymers00
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8650 Å2
ΔGint-49 kcal/mol
Surface area11340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.633, 76.761, 46.010
Angle α, β, γ (deg.)90.000, 103.580, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-134-

HOH

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Components

#1: Protein Transcription factor TCP10


Mass: 11886.519 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TCP10, At2g31070, T16B12.12 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O82277
#2: DNA chain DNA (5'-D(*AP*TP*GP*TP*GP*GP*TP*CP*CP*CP*CP*AP*CP*T)-3')


Mass: 4231.753 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*AP*GP*TP*GP*GP*GP*GP*AP*CP*CP*AP*CP*A)-3')


Mass: 4329.830 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 1.98 Å3/Da / Density % sol: 37.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 10% (w/v) PEG 1000, 10% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.92→44.723 Å / Num. obs: 19285 / % possible obs: 99.77 % / Redundancy: 6.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.1028 / Rpim(I) all: 0.04303 / Rrim(I) all: 0.1116 / Net I/σ(I): 13.65
Reflection shellResolution: 1.92→1.989 Å / Rmerge(I) obs: 0.4344 / Num. unique obs: 1888 / CC1/2: 0.866 / Rpim(I) all: 0.2063 / Rrim(I) all: 0.4821

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
PHENIXmodel building
PHENIXphasing
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VP1

7vp1


Resolution: 1.92→44.72 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.21 --
Rwork0.18 --
obs-19272 99.8 %
Displacement parametersBiso max: 99.89 Å2 / Biso mean: 34.7313 Å2 / Biso min: 12.91 Å2
Refinement stepCycle: LAST / Resolution: 1.92→44.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1137 568 0 114 1819

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