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Yorodumi- PDB-8u46: Crystal structure of Bacteroides thetaiotaomicron VPI-5482 Endogl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8u46 | ||||||
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Title | Crystal structure of Bacteroides thetaiotaomicron VPI-5482 Endoglycosidase BT1285 D161A-E163A inactive version | ||||||
Components | Endo-beta-N-acetylglucosaminidase | ||||||
Keywords | HYDROLASE / Endoglycosidase / artificial lectin / high mannose specific / Bacteroides | ||||||
Function / homology | Function and homology information mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity / carbohydrate metabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Bacteroides thetaiotaomicron VPI-5482 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Sastre, D.E. / Sultana, N. / Sundberg, E.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2024 Title: Human gut microbes express functionally distinct endoglycosidases to metabolize the same N-glycan substrate. Authors: Sastre, D.E. / Sultana, N. / V A S Navarro, M. / Huliciak, M. / Du, J. / Cifuente, J.O. / Flowers, M. / Liu, X. / Lollar, P. / Trastoy, B. / Guerin, M.E. / Sundberg, E.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8u46.cif.gz | 67.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8u46.ent.gz | 47 KB | Display | PDB format |
PDBx/mmJSON format | 8u46.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8u46_validation.pdf.gz | 405.2 KB | Display | wwPDB validaton report |
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Full document | 8u46_full_validation.pdf.gz | 406.3 KB | Display | |
Data in XML | 8u46_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | 8u46_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u4/8u46 ftp://data.pdbj.org/pub/pdb/validation_reports/u4/8u46 | HTTPS FTP |
-Related structure data
Related structure data | 8u47C 8u48C 8u9fC 8w01C 8w04C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30353.545 Da / Num. of mol.: 1 / Mutation: D161A, E163A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria) Gene: BT_1285 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8A889 |
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#2: 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: 2.04 Å3/Da / Density % sol: 39.57 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop Details: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD 0.03 M of each divalent cation 0.1 M MOPS/HEPES-Na pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 16, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 14793 / % possible obs: 98.35 % / Redundancy: 6 % / CC1/2: 0.985 / CC star: 0.996 / Rpim(I) all: 0.057 / Rrim(I) all: 0.188 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.1→2.18 Å / Mean I/σ(I) obs: 0.7 / Num. unique obs: 6926 / CC1/2: 0.899 / CC star: 0.973 / Rpim(I) all: 0.184 / Rrim(I) all: 0.57 / Χ2: 0.674 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→49.77 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.05 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→49.77 Å
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Refine LS restraints |
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LS refinement shell |
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