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- PDB-7vp6: Structure of a transcription factor and DNA complex -

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Basic information

Entry
Database: PDB / ID: 7vp6
TitleStructure of a transcription factor and DNA complex
ComponentsTranscription factor TCP15
KeywordsDNA BINDING PROTEIN / Complex / Transcription factor / TRANSCRIPTION / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


stamen filament development / regulation of anthocyanin biosynthetic process / gynoecium development / DNA endoreduplication / inflorescence development / response to cytokinin / circadian rhythm / transcription cis-regulatory region binding / DNA-binding transcription factor activity / cell division ...stamen filament development / regulation of anthocyanin biosynthetic process / gynoecium development / DNA endoreduplication / inflorescence development / response to cytokinin / circadian rhythm / transcription cis-regulatory region binding / DNA-binding transcription factor activity / cell division / regulation of DNA-templated transcription / nucleus
Similarity search - Function
Transcription factor, TCP / Transcription factor TCP subgroup / TCP family transcription factor / TCP domain profile.
Similarity search - Domain/homology
Transcription factor TCP15
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 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
D: Transcription factor TCP15
J: Transcription factor TCP15


Theoretical massNumber of molelcules
Total (without water)14,7412
Polymers14,7412
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-31 kcal/mol
Surface area5130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.628, 51.634, 71.031
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Transcription factor TCP15 / AtTCP15


Mass: 7370.460 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TCP15, At1g69690, T6C23.11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9C9L2

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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: 1.66 Å3/Da / Density % sol: 26.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 60% v/v Tacsimate pH 7.0

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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: Jun 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.57→29.26 Å / Num. obs: 3381 / % possible obs: 99.06 % / Redundancy: 11.7 % / Rmerge(I) obs: 0.08843 / Net I/σ(I): 26.39
Reflection shellResolution: 2.57→2.661 Å / Rmerge(I) obs: 0.2649 / Num. unique obs: 305

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
PHENIXmodel building
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VP3

7vp3


Resolution: 2.57→29.26 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / Phase error: 25.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2651 596 -
Rwork0.1844 5375 -
obs-3381 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.14 Å2 / Biso mean: 35.6112 Å2 / Biso min: 21.82 Å2
Refinement stepCycle: final / Resolution: 2.57→29.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms652 0 0 0 652
Num. residues----91
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007668
X-RAY DIFFRACTIONf_angle_d0.812907
X-RAY DIFFRACTIONf_chiral_restr0.044108
X-RAY DIFFRACTIONf_plane_restr0.004117
X-RAY DIFFRACTIONf_dihedral_angle_d3.839401
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.57-2.82620.34971400.2144128996
2.8262-3.23470.28261530.21151374100
3.2347-4.07360.271500.16871347100
4.0736-29.260.23681530.16671365100

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