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Open data
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Basic information
Entry | Database: PDB / ID: 7vp4 | |||||||||
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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 | ![]() | 258.3 KB | Display | ![]() |
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PDB format | ![]() | 201.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 506.2 KB | Display | ![]() |
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Full document | ![]() | 514.4 KB | Display | |
Data in XML | ![]() | 17.8 KB | Display | |
Data in CIF | ![]() | 24.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7vp1C ![]() 7vp2C ![]() 7vp3SC ![]() 7vp5C ![]() 7vp6C ![]() 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 11886.519 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: DNA chain | Mass: 4271.777 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | Mass: 4289.805 Da / Num. of mol.: 3 / 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: 2.38 Å3/Da / Density % sol: 48.22 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 100mM Sodium HEPES pH 7.0, 10% w/v PEG 4000 and 10% v/v 2-Propanol |
-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: Nov 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 3.04→29.16 Å / Num. obs: 17509 / % possible obs: 97.13 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.1001 / Net I/σ(I): 14.46 |
Reflection shell | Resolution: 3.04→3.149 Å / Rmerge(I) obs: 0.4615 / Num. unique obs: 1650 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7VP3 Resolution: 3.04→29.16 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / Phase error: 28.43 / 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: 158.32 Å2 / Biso mean: 67.3689 Å2 / Biso min: 20 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.04→29.16 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: 76.3114 Å / Origin y: -7.4791 Å / Origin z: 130.8704 Å
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Refinement TLS group |
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