+Open data
-Basic information
Entry | Database: PDB / ID: 7nek | ||||||
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Title | SusD protein from human gut uncultured Bacteroides | ||||||
Components | RagB SusD domain containing protein | ||||||
Keywords | TRANSPORT PROTEIN / nutrients / entry / oligosaccharides / transporter | ||||||
Function / homology | SusD-like, N-terminal / Starch-binding associating with outer membrane / RagB/SusD domain / SusD family / cell outer membrane / Tetratricopeptide-like helical domain superfamily / RagB SusD domain containing protein Function and homology information | ||||||
Biological species | uncultured bacterium (environmental samples) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Cioci, C. / Tauzin, A. / Wang, Z. / Machado, B. / Lippens, G. / Potocki-Veronese, G. | ||||||
Citation | Journal: To Be Published Title: SusD protein from human gut uncultured Bacteroides Authors: Cioci, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7nek.cif.gz | 255.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nek.ent.gz | 205.8 KB | Display | PDB format |
PDBx/mmJSON format | 7nek.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ne/7nek ftp://data.pdbj.org/pub/pdb/validation_reports/ne/7nek | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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: 68978.820 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured bacterium (environmental samples) Production host: Escherichia coli (E. coli) / References: UniProt: S6CP61 |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.31 Å3/Da / Density % sol: 76.83 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, sitting drop / Details: 1.7M Na3Citrate, 15% Glycerol, 0.1M HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 27, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→127.73 Å / Num. obs: 43113 / % possible obs: 100 % / Redundancy: 7.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.062 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.65→2.79 Å / Rmerge(I) obs: 0.736 / Num. unique obs: 6221 / CC1/2: 0.86 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: from Morda server Resolution: 2.65→127.73 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 20.388 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 85.816 Å2
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Refinement step | Cycle: 1 / Resolution: 2.65→127.73 Å
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Refine LS restraints |
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