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- PDB-7vp1: Structure of a transcription factor and DNA complex -

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Basic information

Entry
Database: PDB / ID: 7vp1
TitleStructure of a transcription factor and DNA complex
Components
  • DNA (5'-D(*AP*TP*GP*TP*GP*GP*TP*CP*CP*CP*CP*C)-3')
  • DNA (5'-D(*TP*GP*GP*GP*GP*GP*AP*CP*CP*AP*CP*A)-3')
  • Transcription factor TCP10
KeywordsDNA BINDING PROTEIN / Complex / Transcription factor / TRANSCRIPTION
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 / SAD / Resolution: 2.902 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription factor TCP10
B: Transcription factor TCP10
C: DNA (5'-D(*AP*TP*GP*TP*GP*GP*TP*CP*CP*CP*CP*C)-3')
D: DNA (5'-D(*TP*GP*GP*GP*GP*GP*AP*CP*CP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)31,4174
Polymers31,4174
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8300 Å2
ΔGint-52 kcal/mol
Surface area9250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.123, 68.123, 210.819
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Transcription factor TCP10


Mass: 12045.242 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) / References: UniProt: O82277
#2: DNA chain DNA (5'-D(*AP*TP*GP*TP*GP*GP*TP*CP*CP*CP*CP*C)-3')


Mass: 3614.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*GP*GP*GP*GP*GP*AP*CP*CP*AP*CP*A)-3')


Mass: 3712.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has ligand of interestN

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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: 2.27 Å3/Da / Density % sol: 45.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Potassium sodium tartrate tetrahydrate, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.902→29.21 Å / Num. obs: 6982 / % possible obs: 99.52 % / Redundancy: 20 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1173 / Rpim(I) all: 0.01942 / Rrim(I) all: 0.1189 / Net I/σ(I): 38.48
Reflection shellResolution: 2.902→3.006 Å / Rmerge(I) obs: 0.6148 / Num. unique obs: 653 / CC1/2: 0.975 / Rpim(I) all: 0.09861 / Rrim(I) all: 0.6228

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
XDSdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.902→29.21 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / Phase error: 20.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2385 1215 10.05 %
Rwork0.1778 10872 -
obs0.1838 6982 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.5 Å2 / Biso mean: 49.7307 Å2 / Biso min: 16.88 Å2
Refinement stepCycle: final / Resolution: 2.902→29.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms956 486 0 0 1442
Num. residues----143
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081518
X-RAY DIFFRACTIONf_angle_d0.9412143
X-RAY DIFFRACTIONf_chiral_restr0.057235
X-RAY DIFFRACTIONf_plane_restr0.006190
X-RAY DIFFRACTIONf_dihedral_angle_d19.788827
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.902-3.01780.25671340.1872118297
3.0178-3.1550.32381360.20991203100
3.155-3.32110.24291340.1821211100
3.3211-3.52890.24431370.17881210100
3.5289-3.80080.31241340.19471235100
3.8008-4.18230.23371370.17441194100
4.1823-4.78530.18071340.14851212100
4.7853-6.02050.23571340.17431210100
6.0205-29.210.20741350.18041215100
Refinement TLS params.Method: refined / Origin x: 0.6027 Å / Origin y: 23.5675 Å / Origin z: 4.5119 Å
111213212223313233
T0.0905 Å20.0292 Å20.0925 Å2-0.3343 Å20.0673 Å2--0.2216 Å2
L1.713 °20.8467 °20.2001 °2-1.4041 °2-0.2308 °2--1.3605 °2
S-0.0433 Å °-0.0936 Å °-0.0753 Å °-0.0032 Å °-0.014 Å °-0.0625 Å °0.164 Å °0.0375 Å °0.0058 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA21 - 86
2X-RAY DIFFRACTION1allB32 - 85
3X-RAY DIFFRACTION1allC1 - 12
4X-RAY DIFFRACTION1allD1 - 12

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