+Open data
-Basic information
Entry | Database: PDB / ID: 7vp3 | |||||||||
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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 | |||||||||
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 / 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 | Arabidopsis thaliana (thale cress) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.003 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 | 7vp3.cif.gz | 283 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vp3.ent.gz | 223.5 KB | Display | PDB format |
PDBx/mmJSON format | 7vp3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vp/7vp3 ftp://data.pdbj.org/pub/pdb/validation_reports/vp/7vp3 | HTTPS FTP |
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-Related structure data
Related structure data | 7vp1C 7vp2SC 7vp4C 7vp5C 7vp6C 7vp7C 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3672.406 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Protein | Mass: 8159.337 Da / Num. of mol.: 8 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 #3: DNA chain | Mass: 3654.378 Da / Num. of mol.: 4 / 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: 3.33 Å3/Da / Density % sol: 68.47 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 100 mM Sodium citrate/Citric acid pH 5.5, 20% 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: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 11, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 3.003→18.17 Å / Num. obs: 25799 / % possible obs: 93.27 % / Redundancy: 25.9 % / Rmerge(I) obs: 0.2602 / Rrim(I) all: 0.2654 / Net I/σ(I): 19.26 |
Reflection shell | Resolution: 3.003→3.11 Å / Rmerge(I) obs: 0.8339 / Num. unique obs: 1836 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7VP2 Resolution: 3.003→18.17 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.7 / 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: 133.52 Å2 / Biso mean: 60.8407 Å2 / Biso min: 20 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.003→18.17 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: 9.3478 Å / Origin y: -22.94 Å / Origin z: -38.741 Å
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Refinement TLS group |
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