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Yorodumi- PDB-1jpc: MANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM SNOWDROP (GALANTHUS NIV... -
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-Basic information
Entry | Database: PDB / ID: 1jpc | |||||||||
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Title | MANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM SNOWDROP (GALANTHUS NIVALIS) BULBS IN COMPLEX WITH MANNOSE-ALPHA1,6-(MANNOSE-ALPHA1,3)-MANNOSE-ALPHA1,6-(MANNOSE-ALPHA1,3)-MANNOSE | |||||||||
Components | AGGLUTININ | |||||||||
Keywords | LECTIN / AGGLUTININ / MANNOPENTAOSE / (MANNOSE-ALPHA1 / 6-(MANNOSE-ALPHA1 / 3-MANNOSE- ALPHA1 / 3)-MANNOSE) / SNOWDROP | |||||||||
Function / homology | Function and homology information regulation of defense response to virus / D-mannose binding / response to virus / defense response / extracellular region Similarity search - Function | |||||||||
Biological species | Galanthus nivalis (common snowdrop) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | |||||||||
Authors | Wright, C.S. / Hester, G. | |||||||||
Citation | Journal: Structure / Year: 1996 Title: The 2.0 A structure of a cross-linked complex between snowdrop lectin and a branched mannopentaose: evidence for two unique binding modes. Authors: Wright, C.S. / Hester, G. #1: Journal: J.Mol.Biol. / Year: 1996 Title: The Mannose-Specific Bulb Lectin from Galanthus Nivalis (Snowdrop) Binds Mono-and Dimannosides at Distinct Sites. Structure Analysis of Refined Complexes at 2.3 A and 3.0 A Resolution Authors: Hester, G. / Wright, C.S. #2: Journal: Nat.Struct.Biol. / Year: 1995 Title: Structure of Mannose-Specific Snowdrop (Galanthus Nivalis) Lectin is Representative of a New Plant Lectin Family Authors: Hester, G. / Kaku, H. / Goldstein, I.J. / Wright, C.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jpc.cif.gz | 33.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jpc.ent.gz | 26.4 KB | Display | PDB format |
PDBx/mmJSON format | 1jpc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jp/1jpc ftp://data.pdbj.org/pub/pdb/validation_reports/jp/1jpc | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 12061.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: THE SNOWDROP IS A REPRESENTATIVE OF THE PLANT FAMILY OF AMARYLLIDACEAE. THE PROTEIN IS ISOLATED FROM THE BULBS. Source: (natural) Galanthus nivalis (common snowdrop) / References: UniProt: P30617 | ||||
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#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose / 6alpha-alpha-mannobiose | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 57 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jul 7, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 11166 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.074 |
Reflection | *PLUS Num. measured all: 54560 |
Reflection shell | *PLUS Highest resolution: 2 Å / Lowest resolution: 2.05 Å / % possible obs: 99.6 % |
-Processing
Software |
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Refinement | Resolution: 2→8 Å / σ(F): 0
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Displacement parameters | Biso mean: 33.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.22 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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