+Open data
-Basic information
Entry | Database: PDB / ID: 5yuh | ||||||
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Title | AtVAL1 PHD-Like domain in the P6122 space group | ||||||
Components | B3 domain-containing transcription repressor VAL1 | ||||||
Keywords | STRUCTURAL PROTEIN / AtVAL1 / PHD-Like domain / PHD | ||||||
Function / homology | Function and homology information response to abscisic acid / response to sucrose / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / mitochondrion / DNA binding / zinc ion binding / nucleus Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.801 Å | ||||||
Authors | Zhang, M.M. / Wu, B.X. | ||||||
Citation | Journal: To Be Published Title: AtVAL1 PHD-Like domain in the P6122 space group Authors: Zhang, M.M. / Wu, B.X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yuh.cif.gz | 31.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yuh.ent.gz | 19.6 KB | Display | PDB format |
PDBx/mmJSON format | 5yuh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yuh_validation.pdf.gz | 418 KB | Display | wwPDB validaton report |
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Full document | 5yuh_full_validation.pdf.gz | 418.5 KB | Display | |
Data in XML | 5yuh_validation.xml.gz | 5.4 KB | Display | |
Data in CIF | 5yuh_validation.cif.gz | 6.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yu/5yuh ftp://data.pdbj.org/pub/pdb/validation_reports/yu/5yuh | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 12261.192 Da / Num. of mol.: 1 / Fragment: PHD-Like domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: VAL1, HSI2, At2g30470, T6B20.17 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8W4L5 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.15M DL-Malic acid pH 7.0, 20% w/v Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97737 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97737 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 10206 / % possible obs: 99.9 % / Redundancy: 33.7 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 48.25 |
Reflection shell | Resolution: 1.8→1.86 Å |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.801→26.371 Å / SU ML: 0.22 / Cross valid method: NONE / σ(F): 1.38 / Phase error: 29.06
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.801→26.371 Å
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Refine LS restraints |
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LS refinement shell |
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