+Open data
-Basic information
Entry | Database: PDB / ID: 5lx8 | ||||||
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Title | Crystal structure of BT1762 | ||||||
Components | SusD homolog | ||||||
Keywords | TRANSPORT PROTEIN / outer membrane protein / protein complex / TonB dependent transporter / carbohydrate binding protein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.76 Å | ||||||
Authors | Basle, A. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nature / Year: 2017 Title: Structural basis for nutrient acquisition by dominant members of the human gut microbiota. Authors: Glenwright, A.J. / Pothula, K.R. / Bhamidimarri, S.P. / Chorev, D.S. / Basle, A. / Firbank, S.J. / Zheng, H. / Robinson, C.V. / Winterhalter, M. / Kleinekathofer, U. / Bolam, D.N. / van den Berg, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lx8.cif.gz | 125.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lx8.ent.gz | 100.5 KB | Display | PDB format |
PDBx/mmJSON format | 5lx8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lx/5lx8 ftp://data.pdbj.org/pub/pdb/validation_reports/lx/5lx8 | HTTPS FTP |
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-Related structure data
Related structure data | 5fq3C 5fq4C 5fq6C 5fq7C 5fq8C 5t3rC 5t4yC 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: 65029.414 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria) Gene: BT_1762 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8A6W4 | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 2.0 M ammonium sulfate, 100 mM sodium acetate pH 4.6 and 8% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 5, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→45.7 Å / Num. obs: 59338 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.091 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.76→1.79 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.9 / CC1/2: 0.59 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.76→45.7 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.315 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.098 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.05 Å2
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Refinement step | Cycle: 1 / Resolution: 1.76→45.7 Å
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Refine LS restraints |
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