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Yorodumi- PDB-7bbi: Joint X-ray/neutron room temperature structure of H/D-exchanged P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bbi | ||||||
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Title | Joint X-ray/neutron room temperature structure of H/D-exchanged PLL lectin | ||||||
Components | PLL lectin | ||||||
Keywords | SUGAR BINDING PROTEIN / propeller | ||||||
Function / homology | Protein of unknown function DUF346 / Repeat of unknown function (DUF346) / Uncharacterized protein Function and homology information | ||||||
Biological species | Photorhabdus laumondii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / NEUTRON DIFFRACTION / SYNCHROTRON / NUCLEAR REACTOR / 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 | 7bbi.cif.gz | 219 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bbi.ent.gz | 146.6 KB | Display | PDB format |
PDBx/mmJSON format | 7bbi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bbi_validation.pdf.gz | 394.5 KB | Display | wwPDB validaton report |
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Full document | 7bbi_full_validation.pdf.gz | 394.9 KB | Display | |
Data in XML | 7bbi_validation.xml.gz | 9.4 KB | Display | |
Data in CIF | 7bbi_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bb/7bbi ftp://data.pdbj.org/pub/pdb/validation_reports/bb/7bbi | HTTPS FTP |
-Related structure data
Related structure data | 7b7cC 7b7eC 7b7fC 7bb4C 7bbcC 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: Water | ChemComp-HOH / |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment |
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-Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M sodium acetate, pD 4.2, 8 % (w/v) PEG 4000 dissolved in D2O |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Biso Wilson estimate: 20.07 Å2 / Entry-ID: 7BBI
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Reflection shell |
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-Processing
Software |
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Refinement |
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Refinement step | Cycle: LAST / Resolution: 1.7→39.84 Å
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Refine LS restraints |
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LS refinement shell |
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