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Yorodumi- PDB-2vud: PA-IIL lectin from pseudomonas aeruginosa complexed with fucose- ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vud | ||||||
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Title | PA-IIL lectin from pseudomonas aeruginosa complexed with fucose- derived glycomimetics | ||||||
Components | FUCOSE-BINDING LECTIN PA-IIL | ||||||
Keywords | SUGAR BINDING PROTEIN / LECTIN / PSEUDOMONAS AERUGINOSA / GLYCOMIMETICS / FUCOSE / SUGAR-BINDING PROTEIN | ||||||
Function / homology | Function and homology information single-species biofilm formation / carbohydrate binding / metal ion binding Similarity search - Function | ||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Beha, S. / Marotte, K. / Sabin, C. / Mitchell, E.P. / Imberty, A. / Roy, R. | ||||||
Citation | Journal: To be Published Title: Fucose-Derived Glycomimetics as High Affinity Ligands for Bacterial Lectin Pa-Iil from Pseudomonas Aeruginosa Authors: Beha, S. / Marotte, K. / Sabin, C. / Mitchell, E.P. / Imberty, A. / Roy, R. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vud.cif.gz | 115.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vud.ent.gz | 88 KB | Display | PDB format |
PDBx/mmJSON format | 2vud.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vu/2vud ftp://data.pdbj.org/pub/pdb/validation_reports/vu/2vud | HTTPS FTP |
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-Related structure data
Related structure data | 2vucC 1uzvS 1w43 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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 11734.707 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-115 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HYN5 |
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-Sugars , 2 types, 4 molecules
#4: Sugar | ChemComp-FUC / |
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#5: Sugar |
-Non-polymers , 3 types, 617 molecules
#2: Chemical | ChemComp-CA / #3: Chemical | #6: 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: 1.88 Å3/Da / Density % sol: 46.17 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: TRIS HCL 0.1M PH8.5, 1.75M AMMNONIUM SULFATE(THE PA-IIL/GLYCOMIMETIC COMPLEX WAS OBTAINED BY SOAKING METHOD FROM FUCOSE-CONTAINING CRYSTAL) |
-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 26, 2006 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: SINGLE CRYSTAL DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→44.11 Å / Num. obs: 46062 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.2 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UZV Resolution: 1.7→55.22 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.925 / SU B: 2.959 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.02 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→55.22 Å
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Refine LS restraints |
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