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Yorodumi- PDB-1w8f: PSEUDOMONAS AERUGINOSA LECTIN II (PA-IIL)COMPLEXED WITH LACTO-N-N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1w8f | |||||||||
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Title | PSEUDOMONAS AERUGINOSA LECTIN II (PA-IIL)COMPLEXED WITH LACTO-N-NEO- FUCOPENTAOSE V(LNPFV) | |||||||||
Components | PSEUDOMONAS AERUGINOSA LECTIN II | |||||||||
Keywords | SUGAR BINDING PROTEIN / PENTASSACHARIDE / CYSTIC FIROSIS INFECTION OF LUNGS | |||||||||
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: 1.05 Å | |||||||||
Authors | Perret, S. / Sabin, C. / Dumon, C. / Budova, M. / Gautier, C. / Galanina, O. / Ilia, S. / Bovin, N. / Nicaise, M. / Desmadril, M. ...Perret, S. / Sabin, C. / Dumon, C. / Budova, M. / Gautier, C. / Galanina, O. / Ilia, S. / Bovin, N. / Nicaise, M. / Desmadril, M. / Gilboa-Garber, N. / Wimmerova, M. / Mitchell, E.P. / Imberty, A. | |||||||||
Citation | 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.P. / Imberty, A. #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. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1w8f.cif.gz | 229.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w8f.ent.gz | 182.6 KB | Display | PDB format |
PDBx/mmJSON format | 1w8f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/1w8f ftp://data.pdbj.org/pub/pdb/validation_reports/w8/1w8f | HTTPS FTP |
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-Related structure data
Related structure data | 1w8hC 1gztS 1w38 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 Details: EACH MONOMER CONTAINS TWO CLOSE CALCIUM CATIONS THAT MEDIATE THE BINDING OF THE SACCHARIDE Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Plasmid: PET25PA2L / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HYN5 |
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-Sugars , 3 types, 4 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
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#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]beta-D-glucopyranose | Source method: isolated from a genetically manipulated source |
-Non-polymers , 4 types, 741 molecules
#5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-CA / #7: Chemical | #8: 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: 2.3 Å3/Da / Density % sol: 45.6 % Description: PHASING WAS PERFORMED WITH ACORN, USING ONLY THE POSITION OF 3 OF THE CALCIUM IONS FROM THE CRYSTAL STRUCTURE OF PA-IIL COMPLEXED WITH FUCOSE PREVIOUSLY SOLVED AT 1 ANG RESOLUTION |
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Crystal grow | pH: 8.5 Details: TRIS HCL 0.1M, PH8.5, 1.75 M AMMNONIUM SULFATE, pH 8.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 4, 2004 / Details: MULTILAYER MIRROR |
Radiation | Monochromator: SINGLE CRYSTAL DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.05→14.51 Å / Num. obs: 180957 / % possible obs: 93.3 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 7 |
Reflection shell | Resolution: 1.05→1.08 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 1.8 / % possible all: 89.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GZT Resolution: 1.05→14.51 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.271 / SU ML: 0.014 / Cross valid method: THROUGHOUT / ESU R: 0.021 / ESU R Free: 0.022 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 7.31 Å2
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Refinement step | Cycle: LAST / Resolution: 1.05→14.51 Å
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Refine LS restraints |
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