+Open data
-Basic information
Entry | Database: PDB / ID: 8hmh | ||||||
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Title | The closed state of RGLG2-VWA | ||||||
Components | E3 ubiquitin-protein ligase RGLG2 | ||||||
Keywords | STRUCTURAL PROTEIN / closed state / calcium ions / PLANT PROTEIN / TRANSFERASE | ||||||
Function / homology | Function and homology information auxin metabolic process / negative regulation of response to water deprivation / cytokinin metabolic process / abscisic acid-activated signaling pathway / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / metal ion binding / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å | ||||||
Authors | Wang, Q. | ||||||
Funding support | China, 1items
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Citation | Journal: Biochim Biophys Acta Proteins Proteom / Year: 2024 Title: The regulation of RGLG2-VWA by Ca 2+ ions. Authors: Zhang, M. / Zhang, J. / Liang, Y. / Tian, S. / Xie, S. / Zhou, T. / Wang, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hmh.cif.gz | 119.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hmh.ent.gz | 90.9 KB | Display | PDB format |
PDBx/mmJSON format | 8hmh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hm/8hmh ftp://data.pdbj.org/pub/pdb/validation_reports/hm/8hmh | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 34425.277 Da / Num. of mol.: 2 / Fragment: VWA domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: RGLG2, At5g14420, F18O22.210 / Production host: Escherichia coli (E. coli) References: UniProt: Q9LY87, RING-type E3 ubiquitin transferase #2: Chemical | ChemComp-MG / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.26 Å3/Da / Density % sol: 44.88 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 200 mM magnesium chloride, 30% PEG 4000, 100 mM Tris-HCl, PH8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: AichiSR / Beamline: BL2S1 / Wavelength: 0.979183 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 5, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979183 Å / Relative weight: 1 |
Reflection | Resolution: 2.56→48.873 Å / Num. obs: 19226 / % possible obs: 99 % / Redundancy: 13.9 % / CC1/2: 0.994 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.56→2.63 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 962 / CC1/2: 0.722 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.56→48.873 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 30.15 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.56→48.873 Å
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Refine LS restraints |
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LS refinement shell |
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