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Open data
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Basic information
Entry | Database: PDB / ID: 7vp7 | |||||||||
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Title | Structure of a transcription factor and DNA complex | |||||||||
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![]() | DNA BINDING PROTEIN / Complex / Transcription factor / TRANSCRIPTION / TRANSCRIPTION-DNA complex | |||||||||
Function / homology | ![]() regulation of secondary shoot formation / leaf senescence / leaf development / sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / nucleus Similarity search - Function | |||||||||
Biological species | ![]() ![]() synthetic construct (others) | |||||||||
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 | ![]() | 83.5 KB | Display | ![]() |
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PDB format | ![]() | 58.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446 KB | Display | ![]() |
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Full document | ![]() | 447.3 KB | Display | |
Data in XML | ![]() | 6.5 KB | Display | |
Data in CIF | ![]() | 7.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7vp1C ![]() 7vp2SC ![]() 7vp3C ![]() 7vp4C ![]() 7vp5C ![]() 7vp6C 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: 11886.519 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: DNA chain | | Mass: 5117.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | | Mass: 5274.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.27 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 100mM Tris pH 8.0 and 20% w/v PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 24, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.653→35.562 Å / Num. obs: 8931 / % possible obs: 96.4 % / Redundancy: 19.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 27.61 |
Reflection shell | Resolution: 2.653→2.748 Å / Rmerge(I) obs: 0.7905 / Num. unique obs: 586 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7VP2 Resolution: 2.653→35.562 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / Phase error: 29.06 / 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: 138.39 Å2 / Biso mean: 41.0638 Å2 / Biso min: 6.31 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.653→35.562 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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Refinement TLS params. | Method: refined / Origin x: 30.2974 Å / Origin y: -21.98 Å / Origin z: 33.6245 Å
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Refinement TLS group |
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