+Open data
-Basic information
Entry | Database: PDB / ID: 5ngk | ||||||
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Title | The endo-beta1,6-glucanase BT3312 | ||||||
Components | Glucosylceramidase | ||||||
Keywords | HYDROLASE / glycoside hydrolase / endo-beta1 / 6-clucanase / beta-1 / 6-glucan / Bacteroides / human gut microbiota / yeast glycan | ||||||
Function / homology | Function and homology information glucosylceramide catabolic process / glucosylceramidase activity / sphingolipid metabolic process Similarity search - Function | ||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Basle, A. / Temple, M. / Cuskin, F. / Lowe, E. / Gilbert, H. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J. Biol. Chem. / Year: 2017 Title: A Bacteroidetes locus dedicated to fungal 1,6-beta-glucan degradation: Unique substrate conformation drives specificity of the key endo-1,6-beta-glucanase. Authors: Temple, M.J. / Cuskin, F. / Basle, A. / Hickey, N. / Speciale, G. / Williams, S.J. / Gilbert, H.J. / Lowe, E.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ngk.cif.gz | 285.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ngk.ent.gz | 229.8 KB | Display | PDB format |
PDBx/mmJSON format | 5ngk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ng/5ngk ftp://data.pdbj.org/pub/pdb/validation_reports/ng/5ngk | HTTPS FTP |
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-Related structure data
Related structure data | 5nglC 3rilS 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 55324.473 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Gene: ERS852430_01553 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A173SYZ2, UniProt: Q8A2J3*PLUS #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 200 mM Sodium Bromide 100 mM Bis Tris Propane pH 6.5 and 20 % PEG 3350. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9794 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 26, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→48.24 Å / Num. obs: 114209 / % possible obs: 97.4 % / Redundancy: 3.8 % / CC1/2: 0.996 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4871 / CC1/2: 0.466 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3RIL Resolution: 1.9→48.24 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.701 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.139 / 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: 33.579 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→48.24 Å
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Refine LS restraints |
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