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Yorodumi- PDB-1en2: UDA TETRASACCHARIDE COMPLEX. CRYSTAL STRUCTURE OF URTICA DIOICA A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1en2 | ||||||||||||
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Title | UDA TETRASACCHARIDE COMPLEX. CRYSTAL STRUCTURE OF URTICA DIOICA AGGLUTININ, A SUPERANTIGEN PRESENTED BY MHC MOLECULES OF CLASS I AND CLASS II | ||||||||||||
Components | AGGLUTININ ISOLECTIN I/AGGLUTININ ISOLECTIN V/ AGGLUTININ ISOLECTIN VI | ||||||||||||
Keywords | SUGAR BINDING PROTEIN / LECTIN / HEVEIN DOMAIN / UDA / SUPERANTIGEN / SACCHARIDE BINDING | ||||||||||||
Function / homology | Function and homology information chitinase / chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / defense response to fungus / cell wall macromolecule catabolic process / carbohydrate binding / killing of cells of another organism / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Urtica dioica (great nettle) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||||||||
Authors | Saul, F.A. / Rovira, P. / Boulot, G. / Van Damme, E.J.M. / Peumans, W.J. / Truffa-Bachi, P. / Bentley, G.A. | ||||||||||||
Citation | Journal: Structure Fold.Des. / Year: 2000 Title: Crystal structure of Urtica dioica agglutinin, a superantigen presented by MHC molecules of class I and class II. Authors: Saul, F.A. / Rovira, P. / Boulot, G. / Damme, E.J. / Peumans, W.J. / Truffa-Bachi, P. / Bentley, G.A. #1: Journal: Plant Mol.Biol. / Year: 1999 Title: Characterisation of Urtica dioica Agglutinin Isolectins and the Encoding Gene Family Authors: Does, M.P. / Ng, D.K. / Dekker, H.L. / Peumans, W.J. / Houterman, P.M. / Van Damme, E.J. / Cornelissen, B.J.C. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1en2.cif.gz | 36.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1en2.ent.gz | 23.3 KB | Display | PDB format |
PDBx/mmJSON format | 1en2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1en2_validation.pdf.gz | 756.4 KB | Display | wwPDB validaton report |
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Full document | 1en2_full_validation.pdf.gz | 758 KB | Display | |
Data in XML | 1en2_validation.xml.gz | 8 KB | Display | |
Data in CIF | 1en2_validation.cif.gz | 10.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/en/1en2 ftp://data.pdbj.org/pub/pdb/validation_reports/en/1en2 | HTTPS FTP |
-Related structure data
Related structure data | 1eisSC 1enmC S: Starting model for refinement C: citing same article (ref.) |
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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: 9350.269 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PURIFIED FROM THE RHIZOMES / Source: (natural) Urtica dioica (great nettle) / References: GenBank: 4138900, UniProt: P11218*PLUS |
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Water | ChemComp-HOH / |
Compound details | The structure comprises two hevein-like domains, each containing a distinct saccharide-binding site. ...The structure comprises two hevein-like domains, each containing a distinct saccharide-binding site. The two binding sites are located at opposite extremities of the molecule. THE N-TERMINAL RESIDUE IS PYRROLIDON |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.25 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6 Details: PEG 6000, sodium acetate, sodium chloride, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 290.0K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS PH range low: 6.5 / PH range high: 5.5 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.4→25 Å / Num. all: 15524 / Num. obs: 15524 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Redundancy: 9.4 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 25.5 | |||||||||||||||
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.328 / Num. unique all: 1473 / % possible all: 94.2 | |||||||||||||||
Reflection | *PLUS Num. obs: 15499 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 94.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EIS Resolution: 1.4→25 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: The structure was determined by molecular replacement methods based on the uncomplexed UDA structure (1EIS). A bulk solvent correction was applied.
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Refinement step | Cycle: LAST / Resolution: 1.4→25 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |