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Yorodumi- PDB-2wra: BclA lectin from Burkholderia cenocepacia complexed with aMan1(aM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wra | |||||||||
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Title | BclA lectin from Burkholderia cenocepacia complexed with aMan1(aMan1- 6)-3Man trisaccharide | |||||||||
Components | LECTIN | |||||||||
Keywords | SUGAR BINDING PROTEIN / BACTERIAL LECTIN / OLIGOSACCHARIDES | |||||||||
Function / homology | Calcium-mediated lectin / Calcium-mediated lectin / Calcium-mediated lectin superfamily / Fucose-binding lectin II (PA-IIL) / Jelly Rolls / Sandwich / Mainly Beta / metal ion binding / Lectin Function and homology information | |||||||||
Biological species | BURKHOLDERIA CENOCEPACIA (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | |||||||||
Authors | Lameignere, E. / Shiao, T.C. / Roy, R. / Wimmerova, M. / Dubreuil, F. / Varrot, A. / Imberty, A. | |||||||||
Citation | Journal: Glycobiology / Year: 2010 Title: Structural Basis of the Affinity for Oligomannosides and Analogs Displayed by Bc2L-A, a Burkholderia Cenocepacia Soluble Lectin. Authors: Lameignere, E. / Shiao, T.C. / Roy, R. / Wimmerova, M. / Dubreuil, F. / Varrot, A. / Imberty, A. | |||||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: PROVIDED BY DEPOSITOR | |||||||||
Remark 700 | SHEET DETERMINATION METHOD: PROVIDED BY DEPOSITOR |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wra.cif.gz | 75.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wra.ent.gz | 54.7 KB | Display | PDB format |
PDBx/mmJSON format | 2wra.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wr/2wra ftp://data.pdbj.org/pub/pdb/validation_reports/wr/2wra | HTTPS FTP |
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-Related structure data
Related structure data | 2wr9C 2vnvS C: citing same article (ref.) 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 13779.034 Da / Num. of mol.: 1 / Fragment: BCLA MONOMER, RESIDUES 2-129 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BURKHOLDERIA CENOCEPACIA (bacteria) / Strain: J2315 Description: DNA FROM BURKHOLDERIA CENOCEPACIA STRAIN J2315 OBTAINED FROM THE CZECH COLLECTION OF MICROORGANISMS AT BRNO Plasmid: PRSET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B4EH87 | ||||||
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#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose Source method: isolated from a genetically manipulated source | ||||||
#3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | Nonpolymer details | ALPHA-D-MANNOSE (MAN): AMAN1-3AMAN1-6MAN TRISACCHAR | |
-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: 42.17 % / Description: NONE |
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Crystal grow | Details: 80% OF THE INITIAL PRECIPITANT SOLUTION (30% PEG IN 0.2M AMMONIUM SULPHATE) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9794999 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 18, 2006 / Details: MIRRORS |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794999 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→57.45 Å / Num. obs: 47704 / % possible obs: 96.5 % / Observed criterion σ(I): 2.4 / Redundancy: 4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 1.1→1.16 Å / Redundancy: 2 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 2.4 / % possible all: 79.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VNV Resolution: 1.1→57.45 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.819 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.224 Å2
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Refinement step | Cycle: LAST / Resolution: 1.1→57.45 Å
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Refine LS restraints |
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