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Yorodumi- PDB-6r35: Structure of the LecB lectin from Pseudomonas aeruginosa strain P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6r35 | |||||||||
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Title | Structure of the LecB lectin from Pseudomonas aeruginosa strain PAO1 in complex with lewis x tetrasaccharide | |||||||||
Components | Fucose-binding lectin PA-IIL | |||||||||
Keywords | SUGAR BINDING PROTEIN / Lectin / carbohydrate / Lewis x / LecB | |||||||||
Function / homology | Function and homology information single-species biofilm formation / carbohydrate binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Lepsik, M. / Sommer, R. / Kuhaudomlarp, S. / Lelimousin, M. / Varrot, A. / Titz, A. / Imberty, A. | |||||||||
Funding support | France, 1items
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Citation | Journal: Eur.J.Med.Chem. / Year: 2019 Title: Induction of rare conformation of oligosaccharide by binding to calcium-dependent bacterial lectin: X-ray crystallography and modelling study. Authors: Lepsik, M. / Sommer, R. / Kuhaudomlarp, S. / Lelimousin, M. / Paci, E. / Varrot, A. / Titz, A. / Imberty, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6r35.cif.gz | 115.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r35.ent.gz | 88.1 KB | Display | PDB format |
PDBx/mmJSON format | 6r35.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6r35_validation.pdf.gz | 5.8 MB | Display | wwPDB validaton report |
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Full document | 6r35_full_validation.pdf.gz | 5.7 MB | Display | |
Data in XML | 6r35_validation.xml.gz | 24.4 KB | Display | |
Data in CIF | 6r35_validation.cif.gz | 35.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r3/6r35 ftp://data.pdbj.org/pub/pdb/validation_reports/r3/6r35 | HTTPS FTP |
-Related structure data
Related structure data | 5a70C 1w8hS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 1 - 114 / Label seq-ID: 1 - 114
NCS ensembles :
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-Components
-Protein / Sugars , 2 types, 8 molecules DABC
#1: Protein | Mass: 11734.707 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: The first methionine was cleaved. / Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: lecB, PA3361 / Plasmid: pET25 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HYN5 #2: Polysaccharide | alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose / Lewis X antigen / beta anomer |
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-Non-polymers , 4 types, 414 molecules
#3: Chemical | ChemComp-CA / #4: Chemical | #5: Chemical | ChemComp-EDO / #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: 2.29 Å3/Da / Density % sol: 46.32 % |
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Crystal grow | Temperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG8K, CaCl2, ammonium sulphate, Tris-HCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→47.87 Å / Num. obs: 39320 / % possible obs: 99.9 % / Redundancy: 5.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.037 / Rrim(I) all: 0.085 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 5 % / Rmerge(I) obs: 0.533 / Num. unique obs: 2332 / CC1/2: 0.852 / Rpim(I) all: 0.262 / Rrim(I) all: 0.596 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1W8H Resolution: 1.8→47.87 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.149 / SU ML: 0.066 / SU R Cruickshank DPI: 0.1059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.106 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 96.61 Å2 / Biso mean: 18.2 Å2 / Biso min: 5.18 Å2
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Refinement step | Cycle: final / Resolution: 1.8→47.87 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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