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Yorodumi- PDB-7psy: X-ray crystal structure of perdeuterated LecB lectin in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7psy | ||||||
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Title | X-ray crystal structure of perdeuterated LecB lectin in complex with perdeuterated fucose | ||||||
Components | Fucose-binding lectin | ||||||
Keywords | SUGAR BINDING PROTEIN / lectin / complex | ||||||
Function / homology | Lectin, sugar-binding / Calcium-mediated lectin / Calcium-mediated lectin superfamily / Fucose-binding lectin II (PA-IIL) / carbohydrate binding / alpha-L-fucopyranose / Fucose-binding lectin Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.9 Å | ||||||
Authors | Gajdos, L. / Blakeley, M.P. / Haertlein, M. / Forsyth, T.V. / Devos, J.M. / Imberty, A. | ||||||
Funding support | France, 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Neutron crystallography reveals mechanisms used by Pseudomonas aeruginosa for host-cell binding. Authors: Gajdos, L. / Blakeley, M.P. / Haertlein, M. / Forsyth, V.T. / Devos, J.M. / Imberty, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7psy.cif.gz | 363.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7psy.ent.gz | 249.3 KB | Display | PDB format |
PDBx/mmJSON format | 7psy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ps/7psy ftp://data.pdbj.org/pub/pdb/validation_reports/ps/7psy | HTTPS FTP |
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-Related structure data
Related structure data | 7prgC 1gztS 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
#1: Protein | Mass: 11865.905 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Gene: lecB, C0044_25260, CAZ10_21840, DT376_00595, DY979_15445, ECC04_10105, EFK27_13700, EGV95_09240, EGY23_15550, IPC669_23070, PA5486_01888, PAERUG_E15_London_28_01_14_00983, PAMH19_1713, RW109_RW109_02453 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A069Q9V4 #2: Sugar | ChemComp-FUC / #3: Chemical | ChemComp-CA / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.22 Å3/Da / Density % sol: 44.72 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris/DCl, pD 7.1, 20% (w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 29, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 0.9→36.5 Å / Num. obs: 270061 / % possible obs: 87.6 % / Redundancy: 6.1 % / Biso Wilson estimate: 8.83 Å2 / CC1/2: 1 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 0.9→0.92 Å / Num. unique obs: 5821 / CC1/2: 0.63 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GZT Resolution: 0.9→36.53 Å / SU ML: 0.0894 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 16.3494 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.89 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.9→36.53 Å
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Refine LS restraints |
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LS refinement shell |
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