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Yorodumi- PDB-5v6j: Glycan binding protein Y3 from mushroom Coprinus comatus possesse... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5v6j | ||||||
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Title | Glycan binding protein Y3 from mushroom Coprinus comatus possesses anti-leukemic activity | ||||||
Components | TMV resistance protein Y3 | ||||||
Keywords | SUGAR BINDING PROTEIN / Glycan binding protein / Lectin | ||||||
Function / homology | TMV resistance protein Y3 Function and homology information | ||||||
Biological species | Coprinus comatus (shaggy mane) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.18 Å | ||||||
Authors | Li, K. / Zhang, P. / Gang, Y. / Xia, C. / Polston, J.E. / Li, G. / Li, S. / Lin, Z. / Yang, L.-J. / Bruner, S.D. / Ding, Y. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: Cytotoxic protein from the mushroom Coprinus comatus possesses a unique mode for glycan binding and specificity. Authors: Zhang, P. / Li, K. / Yang, G. / Xia, C. / Polston, J.E. / Li, G. / Li, S. / Lin, Z. / Yang, L.J. / Bruner, S.D. / Ding, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5v6j.cif.gz | 109.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5v6j.ent.gz | 88.8 KB | Display | PDB format |
PDBx/mmJSON format | 5v6j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5v6j_validation.pdf.gz | 454.3 KB | Display | wwPDB validaton report |
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Full document | 5v6j_full_validation.pdf.gz | 456.4 KB | Display | |
Data in XML | 5v6j_validation.xml.gz | 27.3 KB | Display | |
Data in CIF | 5v6j_validation.cif.gz | 40 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v6/5v6j ftp://data.pdbj.org/pub/pdb/validation_reports/v6/5v6j | 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: 12225.509 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Coprinus comatus (shaggy mane) / Gene: y3 / Plasmid: PPICZAA / Production host: Komagataella pastoris (fungus) / References: UniProt: G3BK00 #2: Chemical | ChemComp-NHE / #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: 1.95 Å3/Da / Density % sol: 35.97 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 16% PEG4000, 10% V/V GLYCEROL, 0.1 M CHES, PH 9.5 / PH range: 9.5-10.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 14, 2014 |
Radiation | Monochromator: DIAMOND(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.179→41.795 Å / Num. obs: 113409 / % possible obs: 90 % / Redundancy: 5 % / Rmerge(I) obs: 0.04129 / Rsym value: 0.04611 / Net I/σ(I): 22.98 |
Reflection shell | Resolution: 1.18→1.22 Å / Redundancy: 4 % / Rmerge(I) obs: 0.2976 / Mean I/σ(I) obs: 4.4 / % possible all: 80 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.18→41.795 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34
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Solvent computation | VDW probe radii: 1.11 Å | ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.18→41.795 Å
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