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- PDB-1ona: CO-CRYSTALS OF CONCANAVALIN A WITH METHYL-3,6-DI-O-(ALPHA-D-MANNO... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ona | |||||||||
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Title | CO-CRYSTALS OF CONCANAVALIN A WITH METHYL-3,6-DI-O-(ALPHA-D-MANNOPYRANOSYL)-ALPHA-D-MANNOPYRANOSIDE | |||||||||
![]() | CONCANAVALIN A | |||||||||
![]() | PLANT LECTIN / MANGANESE / GLYCOPROTEIN | |||||||||
Function / homology | ![]() regulation of defense response to virus / D-mannose binding / defense response / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Bouckaert, J. / Maes, D. / Poortmans, F. / Wyns, L. / Loris, R. | |||||||||
![]() | ![]() Title: A structure of the complex between concanavalin A and methyl-3,6-di-O-(alpha-D-mannopyranosyl)-alpha-D-mannopyranoside reveals two binding modes. Authors: Loris, R. / Maes, D. / Poortmans, F. / Wyns, L. / Bouckaert, J. #1: ![]() Title: Concanavalin a Crystallized in Complex with the Trisaccharide 3,6-Di-O-(Alpha-D-Mannopyranosyl)-Alpha-D-Mannopyranoside Authors: Bouckaert, J. / Poortmans, F. / Wyns, L. #2: ![]() Title: Structural Basis of Trimannoside Recognition by Concanavalin A Authors: Naismith, J.H. / Field, R.A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 190.3 KB | Display | ![]() |
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PDB format | ![]() | 152.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 22.3 KB | Display | |
Data in CIF | ![]() | 33 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5cnaS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | THE ASYMMETRIC UNIT CONTAINS A TETRAMER. |
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Components
#1: Protein | Mass: 25622.385 Da / Num. of mol.: 4 / Source method: isolated from a natural source Details: CO-CRYSTALS OF CONCANAVALIN A WITH METHYL-3,6-DI-O-(ALPHA-D-MANNOPYRANOSYL)-ALPHA-D-MANNOPYRANOSIDE Source: (natural) ![]() ![]() #2: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]methyl alpha-D-mannopyranoside Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.4 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: 13% POLYETHYLENEGLYCOLMETHYLETHER, 40 MM HEPES PH 6.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Mar 13, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→15 Å / Num. obs: 29495 / % possible obs: 71.3 % / Observed criterion σ(I): 0 / Redundancy: 1.5 % / Biso Wilson estimate: 27.8 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.199 / Mean I/σ(I) obs: 3.8 / % possible all: 22.6 |
Reflection | *PLUS Highest resolution: 2.35 Å / Lowest resolution: 8 Å / Num. obs: 28287 / % possible obs: 73 % / Num. measured all: 44422 / Rmerge(I) obs: 0.065 |
Reflection shell | *PLUS Rmerge(I) obs: 0.197 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 5CNA Resolution: 2.35→8 Å / Data cutoff high absF: 74.22 / σ(F): 0
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Displacement parameters | Biso mean: 15.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.35→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.45 Å
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.382 / Rfactor obs: 0.292 |