+Open data
-Basic information
Entry | Database: PDB / ID: 1bxh | |||||||||
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Title | CONCANAVALIN A COMPLEXED TO METHYL ALPHA1-2 MANNOBIOSIDE | |||||||||
Components | Concanavalin-A | |||||||||
Keywords | SUGAR BINDING PROTEIN / CARBOHYDRATE CONFORMATION / CON A SACCHARIDE COMPLEX / MOLECULAR RECOGNITION / THERMODYNAMICS | |||||||||
Function / homology | Function and homology information regulation of defense response to virus / D-mannose binding / defense response / metal ion binding Similarity search - Function | |||||||||
Biological species | Canavalia ensiformis (jack bean) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | |||||||||
Authors | Moothoo, D.N. / Canaan, B. / Field, R.A. / Naismith, J.H. | |||||||||
Citation | Journal: Glycobiology / Year: 1999 Title: Man alpha1-2 Man alpha-OMe-concanavalin A complex reveals a balance of forces involved in carbohydrate recognition. Authors: Moothoo, D.N. / Canan, B. / Field, R.A. / Naismith, J.H. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: A General Method for Co-Crystallisation of Concanavalin a with Carbohydrates Authors: Moothoo, D.N. / Naismith, J.H. #2: Journal: Glycobiology / Year: 1998 Title: Concanavalin a Distorts the B-Glcnac-(1-2)-Man Linkage of B-Glcnac-(1-2)-A-Man- (1-3)-[B-Glcnac-(1-2)-A-Man-(1-6)]-Man Upon Binding, Authors: Moothoo, D.N. / Naismith, J.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bxh.cif.gz | 193.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bxh.ent.gz | 153.3 KB | Display | PDB format |
PDBx/mmJSON format | 1bxh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bxh_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1bxh_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1bxh_validation.xml.gz | 35.7 KB | Display | |
Data in CIF | 1bxh_validation.cif.gz | 48.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bx/1bxh ftp://data.pdbj.org/pub/pdb/validation_reports/bx/1bxh | HTTPS FTP |
-Related structure data
Related structure data | 5cnaS S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 25622.385 Da / Num. of mol.: 4 / Fragment: UNP P02866 residues 164-281, 30-148 / Source method: isolated from a natural source / Source: (natural) Canavalia ensiformis (jack bean) / References: UniProt: P02866 |
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-Sugars , 3 types, 4 molecules
#2: Polysaccharide | methyl alpha-D-galactopyranoside-(1-2)-methyl alpha-D-mannopyranoside Type: oligosaccharide / Mass: 370.349 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | methyl alpha-D-galactopyranoside-(1-2)-methyl alpha-D-galactopyranoside Type: oligosaccharide / Mass: 370.349 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
#6: Sugar |
-Non-polymers , 3 types, 81 molecules
#4: Chemical | ChemComp-MN / #5: Chemical | ChemComp-CA / #7: 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: 2.41 Å3/Da / Density % sol: 49 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: 13.5% PEG 6K, 1.0M LICL, 0.1M TRIS PH 7.0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293.5 K / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 |
Detector | Type: ENRAF-NONIUS / Detector: IMAGE PLATE / Date: Mar 15, 1997 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→25 Å / Num. obs: 26568 / % possible obs: 99.7 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.75→2.8 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.3 / % possible all: 99.8 |
Reflection shell | *PLUS % possible obs: 99.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5CNA Resolution: 2.75→25 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: ONLY PARTIAL MODELS FOR THE LIGAND ARE INCLUDED IN SUBUNITS B AND C DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
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Solvent computation | Bsol: 39.5 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.75→25 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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Software | *PLUS Name: 'CNS' / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.228 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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