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Yorodumi- PDB-8u9f: Crystal structure of Bacteroides thetaiotamicron BT1285 in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8u9f | ||||||
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Title | Crystal structure of Bacteroides thetaiotamicron BT1285 in complex with NaI | ||||||
Components | Endo-beta-N-acetylglucosaminidase | ||||||
Keywords | HYDROLASE / Endoglycosidase / ENGase / GH18 family / Bacteroides thetaiotaomicron / I-SAD | ||||||
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 / SAD / Resolution: 1.08 Å | ||||||
Authors | Sastre, D.E. / Navarro, M.V.A.S. / 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 | 8u9f.cif.gz | 186.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8u9f.ent.gz | 149.4 KB | Display | PDB format |
PDBx/mmJSON format | 8u9f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8u9f_validation.pdf.gz | 11.8 MB | Display | wwPDB validaton report |
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Full document | 8u9f_full_validation.pdf.gz | 11.5 MB | Display | |
Data in XML | 8u9f_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | 8u9f_validation.cif.gz | 26.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u9/8u9f ftp://data.pdbj.org/pub/pdb/validation_reports/u9/8u9f | HTTPS FTP |
-Related structure data
Related structure data | 8u46C 8u47C 8u48C 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: 30455.592 Da / Num. of mol.: 1 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: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-IOD / #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.81 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 0.056 M Sodium phosphate monobasic monohydrate, 1.344 M Potassium phosphate dibasic, pH 8.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.97718 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 7, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97718 Å / Relative weight: 1 |
Reflection | Resolution: 1.08→41.5 Å / Num. obs: 191890 / % possible obs: 90.8 % / Redundancy: 3 % / CC1/2: 0.997 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.08→1.14 Å / Mean I/σ(I) obs: 2.8 / Num. unique obs: 17229 / CC1/2: 0.921 / % possible all: 50.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.08→41.5 Å / SU ML: 0.06 / Cross valid method: NONE / σ(F): 1.93 / Phase error: 10.22 / 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: 1.08→41.5 Å
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Refine LS restraints |
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LS refinement shell |
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