+Open data
-Basic information
Entry | Database: PDB / ID: 5jyk | ||||||
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Title | Deg9 crystal under 289K | ||||||
Components | Protease Do-like 9 | ||||||
Keywords | HYDROLASE / Deg protease | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / serine-type endopeptidase activity / nucleolus / proteolysis / nucleus Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.297 Å | ||||||
Authors | Ouyang, M. / Zhang, L.X. | ||||||
Citation | Journal: Nat Plants / Year: 2017 Title: The crystal structure of Deg9 reveals a novel octameric-type HtrA protease Authors: Ouyang, M. / Li, X. / Zhao, S. / Pu, H. / Shen, J. / Adam, Z. / Clausen, T. / Zhang, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jyk.cif.gz | 196.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jyk.ent.gz | 153.2 KB | Display | PDB format |
PDBx/mmJSON format | 5jyk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jy/5jyk ftp://data.pdbj.org/pub/pdb/validation_reports/jy/5jyk | HTTPS FTP |
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-Related structure data
Related structure data | 5il9SC 5ilaC 5ilbC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 62382.383 Da / Num. of mol.: 2 / Fragment: UNP residues 65-592 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DEGP9, At5g40200, MSN9.10, MSN9.100 / Production host: Escherichia coli (strain K12) (bacteria) / Strain (production host): K12 References: UniProt: Q9FL12, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases #2: Chemical | ChemComp-GOL / | #3: 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: 2.7 Å3/Da / Density % sol: 54.46 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2M Potassium chloride, 0.05M Hepes pH7.5, 35% v/v Pentaerythritol propoxylate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→50 Å / Num. obs: 77263 / % possible obs: 99.9 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 2.1→2.18 Å / Rmerge(I) obs: 0.962 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5IL9 Resolution: 2.297→35.663 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.63 / 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: 101.96 Å2 / Biso mean: 33.1573 Å2 / Biso min: 9.68 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.297→35.663 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18
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