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Yorodumi- PDB-1k7v: Crystal Structure Analysis of crosslinked-WGA3/GlcNAcbeta1,6Galbe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k7v | ||||||||||||
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Title | Crystal Structure Analysis of crosslinked-WGA3/GlcNAcbeta1,6Galbeta1,4Glc | ||||||||||||
Components | agglutinin isolectin 3 | ||||||||||||
Keywords | SUGAR BINDING PROTEIN / Hevein-type fold | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Triticum aestivum (bread wheat) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||||||||
Authors | Muraki, M. / Ishimura, M. / Harata, K. | ||||||||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2002 Title: Interactions of wheat-germ agglutinin with GlcNAc beta 1,6Gal sequence Authors: Muraki, M. / Ishimura, M. / Harata, K. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1995 Title: X-ray structure of wheat germ agglutinin isolectin 3 Authors: Harata, K. / Nagahora, H. / Jigami, Y. #2: Journal: J.Mol.Biol. / Year: 2000 Title: Crystal structures of Urtica dioica agglutinin and its complex with tri-N-acetylchitotriose Authors: Harata, K. / Muraki, M. #3: Journal: Protein Eng. / Year: 2000 Title: Chemically prepared hevein domains: effect of C-terminal truncation and the mutagenesis of aromatic residues on the affinity for chitin Authors: Muraki, M. / Morii, H. / Harata, K. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k7v.cif.gz | 77.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k7v.ent.gz | 57.1 KB | Display | PDB format |
PDBx/mmJSON format | 1k7v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1k7v_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 1k7v_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 1k7v_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 1k7v_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k7/1k7v ftp://data.pdbj.org/pub/pdb/validation_reports/k7/1k7v | 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: 18752.932 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: P10969 #2: Polysaccharide | Source method: isolated from a genetically manipulated source #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: 2.31 Å3/Da / Density % sol: 46.77 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.9 Details: sodium acetate, calcium chloride, Ethanol, pH 4.9, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknownDetails: Harata, K., (1995) Acta Crystallogr., Sect.D, 51, 1013. | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å |
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Detector | Type: ENRAF-NONIUS FAST / Detector: AREA DETECTOR / Date: Dec 31, 2000 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→23.5 Å / Num. obs: 33443 / Observed criterion σ(I): 0 / Redundancy: 2.07 % / Rmerge(I) obs: 0.102 |
Reflection shell | Resolution: 2.2→2.24 Å / Rmerge(I) obs: 0.204 |
Reflection | *PLUS Highest resolution: 2.2 Å / Num. obs: 16716 / % possible obs: 93.2 % / Num. measured all: 33443 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Native WGA3 Resolution: 2.2→8 Å / σ(F): 2 / Details: Average B-value are for protein atoms
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Displacement parameters | Biso mean: 19.13 Å2 | ||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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Refinement | *PLUS σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.232 / Rfactor Rfree: 0.31 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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