+Open data
-Basic information
Entry | Database: PDB / ID: 5yug | ||||||
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Title | AtVAL1 PHD-Like domain in the P31 space group | ||||||
Components | B3 domain-containing transcription repressor VAL1 | ||||||
Keywords | STRUCTURAL PROTEIN / H3K27me3 / PHD / VAL1 / PHD-Like domain / Histone modification | ||||||
Function / homology | Function and homology information response to sucrose / response to abscisic acid / 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: 1.57 Å | ||||||
Authors | Zhang, M.M. / Wu, B.X. | ||||||
Citation | Journal: To Be Published Title: AtVAL1 PHD-Like domain in the P31 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 | 5yug.cif.gz | 90.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yug.ent.gz | 68.6 KB | Display | PDB format |
PDBx/mmJSON format | 5yug.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yu/5yug ftp://data.pdbj.org/pub/pdb/validation_reports/yu/5yug | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 12261.192 Da / Num. of mol.: 4 / 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 #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 1.95 Å3/Da / Density % sol: 37.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2M Ammonium citrate tribasic 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: 1.57→50 Å / Num. obs: 51823 / % possible obs: 99.8 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.142 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.57→1.63 Å |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.57→26.114 Å / SU ML: 0.18 / Cross valid method: NONE / σ(F): 1.98 / Phase error: 22.79
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.57→26.114 Å
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Refine LS restraints |
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LS refinement shell |
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