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Yorodumi- PDB-5dvh: Structure of the Kunitz-type cysteine protease inhibitor PCPI-3 f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dvh | ||||||||||||
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Title | Structure of the Kunitz-type cysteine protease inhibitor PCPI-3 from potato | ||||||||||||
Components | PCPI-3 | ||||||||||||
Keywords | protease inhibitor / Plant Kunitz-family inhibitor | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Solanum tuberosum (potato) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å | ||||||||||||
Authors | Brynda, J. / Mishra, M. / Mares, M. | ||||||||||||
Funding support | Czech Republic, 3items
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Citation | Journal: To Be Published Title: Structure of the Kunitz-type cysteine protease inhibitor PCPI-3 from potato Authors: Brynda, J. / Mishra, M. / Mares, M. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dvh.cif.gz | 50.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dvh.ent.gz | 37.8 KB | Display | PDB format |
PDBx/mmJSON format | 5dvh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dv/5dvh ftp://data.pdbj.org/pub/pdb/validation_reports/dv/5dvh | HTTPS FTP |
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-Related structure data
Related structure data | 5dvd |
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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: 21312.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum tuberosum (potato) / Variant: Karin cultivar / References: UniProt: A0A1I9GEQ4*PLUS | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.7 Å3/Da / Density % sol: 66.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Reservoir: 3 M sodium chloride, 0.1 M sodium acetate pH 5.5 Protein buffer and concentration: 5 mM sodium acetate pH 5.5 Protein concentration = 10 mg/ml protein:reservoir = 1:1 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 27, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→48.37 Å / Num. obs: 30248 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Biso Wilson estimate: 32.094 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 14.49 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→48.37 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.2009 / WRfactor Rwork: 0.1755 / FOM work R set: 0.862 / SU B: 2.15 / SU ML: 0.066 / SU R Cruickshank DPI: 0.0976 / SU Rfree: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 78.12 Å2 / Biso mean: 23.368 Å2 / Biso min: 14.3 Å2
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Refinement step | Cycle: final / Resolution: 1.8→48.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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