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Yorodumi- PDB-7b7f: Room temperature X-ray structure of H/D-exchanged PLL lectin in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7b7f | ||||||
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Title | Room temperature X-ray structure of H/D-exchanged 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: 1.6 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 | 7b7f.cif.gz | 123.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b7f.ent.gz | 77.1 KB | Display | PDB format |
PDBx/mmJSON format | 7b7f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/7b7f ftp://data.pdbj.org/pub/pdb/validation_reports/b7/7b7f | HTTPS FTP |
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-Related structure data
Related structure data | 7b7cC 7b7eC 7bb4C 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-FUC / #3: Sugar | ChemComp-FUL / #4: 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: 3.08 Å3/Da / Density % sol: 60 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.4 M Na/K tartrate dissolved in D2O, soaked with 50 mM L-fucose dissolved in D2O |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9796 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 24, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→46 Å / Num. obs: 67576 / % possible obs: 98.7 % / Redundancy: 5.2 % / Biso Wilson estimate: 19.77 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.6→1.64 Å / Num. unique obs: 4953 / CC1/2: 0.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5c9o Resolution: 1.6→39.82 Å / SU ML: 0.2352 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.2839 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: 22.55 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→39.82 Å
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Refine LS restraints |
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LS refinement shell |
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