+Open data
-Basic information
Entry | Database: PDB / ID: 5ila | ||||||
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Title | Deg9 protease domain | ||||||
Components | Protease Do-like 9 | ||||||
Keywords | HYDROLASE / protease domain | ||||||
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: 3.001 Å | ||||||
Authors | Ouyang, M. / Liu, L. / Li, X.Y. / Zhao, S. / 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 | 5ila.cif.gz | 91.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ila.ent.gz | 66 KB | Display | PDB format |
PDBx/mmJSON format | 5ila.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ila_validation.pdf.gz | 445.3 KB | Display | wwPDB validaton report |
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Full document | 5ila_full_validation.pdf.gz | 447.9 KB | Display | |
Data in XML | 5ila_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 5ila_validation.cif.gz | 20.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/il/5ila ftp://data.pdbj.org/pub/pdb/validation_reports/il/5ila | HTTPS FTP |
-Related structure data
Related structure data | 5il9SC 5ilbC 5jykC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 32592.357 Da / Num. of mol.: 2 / Fragment: protease domain, UNP residues 65-327 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 (E. coli) References: UniProt: Q9FL12, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases #2: 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: 2.69 Å3/Da / Density % sol: 54.27 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2M Ammonium formate, 0.1M Hepes pH7.5 |
-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: Apr 13, 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: 3→50 Å / Num. obs: 14624 / % possible obs: 100 % / Redundancy: 14.2 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 22.7 |
Reflection shell | Resolution: 3→3.11 Å / Rmerge(I) obs: 0.862 |
-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: 3.001→38.924 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.07
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.35 Å2 / Biso mean: 30.85 Å2 / Biso min: 7.61 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.001→38.924 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: 5
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