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Yorodumi- PDB-2pr0: Crystal structure of Sylvaticin, a new secreted protein from Pyth... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pr0 | ||||||
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Title | Crystal structure of Sylvaticin, a new secreted protein from Pythium Sylvaticum | ||||||
Components | sylvaticin | ||||||
Keywords | TOXIN / elicitin | ||||||
Function / homology | Function and homology information symbiont-mediated perturbation of host defense-related programmed cell death / extracellular region Similarity search - Function | ||||||
Biological species | Pythium sylvaticum (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.72 Å | ||||||
Authors | Lascombe, M.B. / Prange, T. / Retailleau, P. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2007 Title: Structure of sylvaticin, a new alpha-elicitin-like protein from Pythium sylvaticum. Authors: Lascombe, M.B. / Retailleau, P. / Ponchet, M. / Industri, B. / Blein, J.P. / Prange, T. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Purification, crystallization and preliminary X-ray studies of sylvaticin, an elicitin-like protein from Pythium sylvaticum Authors: Lascombe, M.-B. / Ponchet, M. / Cardin, L. / Milat, M.-L. / Blein, J.-P. / Prange, T. | ||||||
History |
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Remark 999 | sequence The sequence of this protein is not available in the UNP database at the time of processing |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pr0.cif.gz | 50.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pr0.ent.gz | 38.9 KB | Display | PDB format |
PDBx/mmJSON format | 2pr0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2pr0_validation.pdf.gz | 451.9 KB | Display | wwPDB validaton report |
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Full document | 2pr0_full_validation.pdf.gz | 454.7 KB | Display | |
Data in XML | 2pr0_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 2pr0_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pr/2pr0 ftp://data.pdbj.org/pub/pdb/validation_reports/pr/2pr0 | HTTPS FTP |
-Related structure data
-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: 10411.029 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pythium sylvaticum (eukaryote) / Strain: strain 37 / References: UniProt: D0VWX7*PLUS #2: Chemical | #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: 2.11 Å3/Da / Density % sol: 41.82 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG 2000 MME, 0.01M NiCl2, 0.1M Tris-HKL pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.480, 1.239 | |||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 14, 2003 / Details: mirrors | |||||||||
Radiation | Monochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.72→26 Å / Num. obs: 18321 / % possible obs: 92.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.048 / Net I/σ(I): 24.2 | |||||||||
Reflection shell | Resolution: 1.72→1.82 Å / Rmerge(I) obs: 0.073 / Mean I/σ(I) obs: 12.5 / % possible all: 71.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.72→25.9 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 19.444 Å2 | ||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.18 Å / Luzzati sigma a obs: 0.11 Å | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.72→25.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.72→1.78 Å
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