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Yorodumi- PDB-7bb4: Crystal structure of perdeuterated PLL lectin in complex with L-fucose -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bb4 | ||||||
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Title | Crystal structure of perdeuterated PLL lectin in complex with L-fucose | ||||||
Components | PLL lectin | ||||||
Keywords | SUGAR BINDING PROTEIN / Complex / propeller | ||||||
Function / homology | Protein of unknown function DUF346 / Repeat of unknown function (DUF346) / alpha-L-fucopyranose / beta-L-fucopyranose / Uncharacterized protein Function and homology information | ||||||
Biological species | Photorhabdus laumondii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Gajdos, L. / Blakeley, M.P. / Kumar, A. / Wimmerova, M. / Haertlein, M. / Forsyth, V.T. / Imberty, A. / Devos, J.M. | ||||||
Funding support | France, 1items
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Citation | Journal: Structure / Year: 2021 Title: Visualization of hydrogen atoms in a perdeuterated lectin-fucose complex reveals key details of protein-carbohydrate interactions. Authors: Gajdos, L. / Blakeley, M.P. / Kumar, A. / Wimmerova, M. / Haertlein, M. / Forsyth, V.T. / Imberty, A. / Devos, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bb4.cif.gz | 130.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bb4.ent.gz | 82.3 KB | Display | PDB format |
PDBx/mmJSON format | 7bb4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bb/7bb4 ftp://data.pdbj.org/pub/pdb/validation_reports/bb/7bb4 | HTTPS FTP |
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-Related structure data
Related structure data | 7b7cC 7b7eC 7b7fC 7bbcC 7bbiC 5c9oS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 41944.949 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Photorhabdus laumondii (bacteria) / Gene: CKY10_20885 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A329WTS5 | ||||||||
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#2: Sugar | ChemComp-FUL / #3: Sugar | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M Na/K tartrate dissolved in D2O, co-crystallized with 50 mM L-fucose dissolved in D2O |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 29, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→56 Å / Num. obs: 55209 / % possible obs: 98 % / Redundancy: 4.2 % / Biso Wilson estimate: 15.7 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 1.7→1.73 Å / Rmerge(I) obs: 0.36 / Num. unique obs: 2949 / CC1/2: 0.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5c9o Resolution: 1.7→45.82 Å / SU ML: 0.1811 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.6421 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: 19.57 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→45.82 Å
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Refine LS restraints |
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LS refinement shell |
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