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Yorodumi- PDB-5ycz: Crystal structure of Alocasin, protease inhibitor from Giant Taro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ycz | ||||||
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Title | Crystal structure of Alocasin, protease inhibitor from Giant Taro (Arum macrorrhizon) | ||||||
Components | Trypsin/chymotrypsin inhibitor | ||||||
Keywords | PLANT PROTEIN / Protease inhibitor / Storage protein / Tubers / Alocasia / Alocasin / Kunitz type | ||||||
Function / homology | Proteinase inhibitor A/B / negative regulation of peptidase activity / Proteinase inhibitor I3, Kunitz legume / Trypsin and protease inhibitor / Soybean trypsin inhibitor (Kunitz) family of protease inhibitors / Kunitz inhibitor STI-like superfamily / serine-type endopeptidase inhibitor activity / Trypsin/chymotrypsin inhibitor Function and homology information | ||||||
Biological species | Alocasia macrorrhizos (giant taro) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.502 Å | ||||||
Authors | Vajravijayan, S. / Pletnev, S. / Nandhagopal, N. / Gunasekaran, K. | ||||||
Citation | Journal: Pest Manag. Sci. / Year: 2018 Title: Crystal structure of a novel Kunitz type inhibitor, alocasin with anti-Aedes aegypti activity targeting midgut proteases. Authors: Vajravijayan, S. / Pletnev, S. / Pletnev, V.Z. / Nandhagopal, N. / Gunasekaran, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ycz.cif.gz | 76.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ycz.ent.gz | 61.1 KB | Display | PDB format |
PDBx/mmJSON format | 5ycz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yc/5ycz ftp://data.pdbj.org/pub/pdb/validation_reports/yc/5ycz | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19793.139 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Alocasia macrorrhizos (giant taro) / References: UniProt: P35812 #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: 2.49 Å3/Da / Density % sol: 50.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES (pH7.5). 1.6 M Ammonium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 7, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→30 Å / Num. obs: 14759 / % possible obs: 99.2 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.042 / Rrim(I) all: 0.104 / Χ2: 0.89 / Net I/σ(I): 8.4 / Num. measured all: 83766 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.502→29.354 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.6 / 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: 93.12 Å2 / Biso mean: 41.3613 Å2 / Biso min: 13.5 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.502→29.354 Å
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