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Yorodumi- PDB-6tcv: Crystal structure of Bacteroides thetaiotamicron EndoBT-3987 in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tcv | |||||||||
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Title | Crystal structure of Bacteroides thetaiotamicron EndoBT-3987 in complex with Man9GlcNAc2Asn substrate | |||||||||
Components | Endo-beta-N-acetylglucosaminidase F1 | |||||||||
Keywords | HYDROLASE / endo-b-N-acetylglucosaminidase / EndoBT / glycoside hydrolase | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Bacteroides thetaiotaomicron VPI-5482 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.311 Å | |||||||||
Authors | Trastoy, B. / Du, J.J. / Klontz, E.H. / Cifuente, J.O. / Sundberg, E.J. / Guerin, M.E. | |||||||||
Citation | Journal: Nat Commun / Year: 2020 Title: Structural basis of mammalian high-mannose N-glycan processing by human gut Bacteroides. Authors: Trastoy, B. / Du, J.J. / Klontz, E.H. / Li, C. / Cifuente, J.O. / Wang, L.X. / Sundberg, E.J. / Guerin, M.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tcv.cif.gz | 247.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tcv.ent.gz | 200.9 KB | Display | PDB format |
PDBx/mmJSON format | 6tcv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tcv_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6tcv_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6tcv_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | 6tcv_validation.cif.gz | 29 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tc/6tcv ftp://data.pdbj.org/pub/pdb/validation_reports/tc/6tcv | HTTPS FTP |
-Related structure data
Related structure data | 6t8iC 6t8kC 6t8lC 6tcwC 3pohS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 49133.781 Da / Num. of mol.: 1 / Mutation: D312A, E314L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria) Gene: BT_3987 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A0N4 |
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#2: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-ASN / |
#4: Chemical | ChemComp-GOL / |
#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: 2.96 Å3/Da / Density % sol: 58.46 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 00 mM M MES pH 6, 50 mM CaCl2 and 10% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97915 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 6, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.31→29.865 Å / Num. obs: 115143 / % possible obs: 99.1 % / Redundancy: 4.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.068 / Net I/σ(I): 10.75 |
Reflection shell | Resolution: 1.31→29.865 Å / Rmerge(I) obs: 0.659 / Mean I/σ(I) obs: 1.33 / Num. unique obs: 10639 / CC1/2: 0.671 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3POH Resolution: 1.311→29.865 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 15.17 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.82 Å2 / Biso mean: 22.4451 Å2 / Biso min: 10.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.311→29.865 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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