+Open data
-Basic information
Entry | Database: PDB / ID: 7vp7 | |||||||||
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Title | Structure of a transcription factor and DNA complex | |||||||||
Components |
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Keywords | DNA BINDING PROTEIN / Complex / Transcription factor / TRANSCRIPTION / TRANSCRIPTION-DNA complex | |||||||||
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 | |||||||||
Biological species | Arabidopsis thaliana (thale cress) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.653 Å | |||||||||
Authors | Zhang, Y. / Xu, Y.P. / Wang, B. / Su, X.D. | |||||||||
Funding support | China, 2items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vp7.cif.gz | 83.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vp7.ent.gz | 58.1 KB | Display | PDB format |
PDBx/mmJSON format | 7vp7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vp/7vp7 ftp://data.pdbj.org/pub/pdb/validation_reports/vp/7vp7 | HTTPS FTP |
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-Related structure data
Related structure data | 7vp1C 7vp2SC 7vp3C 7vp4C 7vp5C 7vp6C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Arabidopsis thaliana (thale cress) / Gene: TCP10, At2g31070, T16B12.12 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O82277 #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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