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Open data
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Basic information
Entry | Database: PDB / ID: 7vp6 | |||||||||
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Title | Structure of a transcription factor and DNA complex | |||||||||
![]() | Transcription factor TCP15 | |||||||||
![]() | DNA BINDING PROTEIN / Complex / Transcription factor / TRANSCRIPTION / TRANSCRIPTION-DNA complex | |||||||||
Function / homology | ![]() stamen filament development / regulation of anthocyanin biosynthetic process / gynoecium development / : / DNA endoreduplication / inflorescence development / response to cytokinin / circadian rhythm / sequence-specific DNA binding / transcription cis-regulatory region binding ...stamen filament development / regulation of anthocyanin biosynthetic process / gynoecium development / : / DNA endoreduplication / inflorescence development / response to cytokinin / circadian rhythm / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity / cell division / regulation of DNA-templated transcription / nucleus Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Zhang, Y. / Xu, Y.P. / Wang, B. / Su, X.D. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for DNA recognition by TCP transcription factors Authors: Zhang, Y. / Xu, Y.P. / Wang, B. / Su, X.D. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 30 KB | Display | ![]() |
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PDB format | ![]() | 17.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7vp1C ![]() 7vp2C ![]() 7vp3SC ![]() 7vp4C ![]() 7vp5C ![]() 7vp7C S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 7370.460 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.66 Å3/Da / Density % sol: 26.1 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 60% v/v Tacsimate pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 6, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 2.57→2.661 Å / Rmerge(I) obs: 0.2649 / Num. unique obs: 305 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7VP3 Resolution: 2.57→29.26 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / Phase error: 25.92 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 87.14 Å2 / Biso mean: 35.6112 Å2 / Biso min: 21.82 Å2 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.57→29.26 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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