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Yorodumi- PDB-2jdh: Lectin PA-IIL of P.aeruginosa complexed with disaccharide derivative -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jdh | |||||||||
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Title | Lectin PA-IIL of P.aeruginosa complexed with disaccharide derivative | |||||||||
Components | FUCOSE-BINDING LECTIN PA-IIL | |||||||||
Keywords | SUGAR BINDING PROTEIN / LECTIN / CYSTIC FIBROSIS | |||||||||
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: 1.1 Å | |||||||||
Authors | Marotte, K. / Sabin, C. / Preville, C. / Pymbock, M. / Deguise, I. / Wimmerova, M. / Mitchell, E.P. / Imberty, A. / Roy, R. | |||||||||
Citation | Journal: Chemmedchem / Year: 2007 Title: X-Ray Structures and Thermodynamics of the Interaction of Pa-Iil from Pseudomonas Aeruginosa with Disaccharide Derivatives. Authors: Marotte, K. / Sabin, C. / Preville, C. / Pymbock, M. / Wimmerova, M. / Mitchell, E.P. / Imberty, A. / Roy, R. #1: Journal: Nat.Struct.Biol. / Year: 2002 Title: Structural Basis for Oligosaccharide-Mediated Adhesion of Pseudomonas Aeruginosa in the Lungs of Cystic Fibrosis Patients Authors: Mitchell, E. / Houles, C. / Sudakevitz, D. / Wimmerova, M. / Gautier, C. / Perez, S. / Wu, A. / Gilboa-Garber, N. / Imberty, A. #2: Journal: Biochem J. / Year: 2005 Title: Structural Basis for the Interaction between Human Milk Oligosaccharides and the Bacterial Lectin Pa-Iil of Pseudomonas Aeruginosa. Authors: Perret, S. / Sabin, C. / Dumon, C. / Pokorna, M. / Gautier, C. / Galanina, O. / Ilia, S. / Bovin, N. / Nicaise, M. / Desmadril, M. / Gilboa-Garber, N. / Wimmerova, M. / Mitchell, E. / Imberty, A. | |||||||||
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 | 2jdh.cif.gz | 219.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jdh.ent.gz | 174.7 KB | Display | PDB format |
PDBx/mmJSON format | 2jdh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jd/2jdh ftp://data.pdbj.org/pub/pdb/validation_reports/jd/2jdh | HTTPS FTP |
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-Related structure data
Related structure data | 2jdkC 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: 11865.905 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HYN5 |
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-Sugars , 2 types, 4 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-FUC / | |
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-Non-polymers , 4 types, 747 molecules
#4: Chemical | ChemComp-CA / #5: Chemical | #6: Chemical | ChemComp-SO4 / | #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: 2.21 Å3/Da / Density % sol: 44.4 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: TRIS HCL 0.1M, PH8.5, 1.75 M AMMNONIUM SULFATE(THE PA-IIL/GLYCOMIMETIC COMPLEXE WAS OBTAINED BY SOAKING METHOD FROM FUCOSE-CONTAINING CRISTAL) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jan 24, 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: 1.1→22.26 Å / Num. obs: 158737 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 1.1→1.3 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 9.4 / % possible all: 92.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UZV Resolution: 1.1→54.23 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.626 / SU ML: 0.014 / Cross valid method: THROUGHOUT / ESU R: 0.024 / ESU R Free: 0.025 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.58 Å2
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Refinement step | Cycle: LAST / Resolution: 1.1→54.23 Å
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Refine LS restraints |
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