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Yorodumi- PDB-6f90: Structure of the family GH92 alpha-mannosidase BT3130 from Bacter... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6f90 | |||||||||
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Title | Structure of the family GH92 alpha-mannosidase BT3130 from Bacteroides thetaiotaomicron in complex with Mannoimidazole (ManI) | |||||||||
Components | Alpha-1,2-mannosidase, putative | |||||||||
Keywords | HYDROLASE / glycan / carbohydrate / glycosidase / substrate specificity / glycoside hydrolase / alpha-mannosidase / GH92 / gut bacteria / microbiota / CAZy / CAZypedia | |||||||||
Function / homology | Function and homology information carbohydrate binding / hydrolase activity / carbohydrate metabolic process Similarity search - Function | |||||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Thompson, A.J. / Spears, R.J. / Zhu, Y. / Suits, M.D.L. / Williams, S.J. / Gilbert, H.J. / Davies, G.J. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2018 Title: Bacteroides thetaiotaomicron generates diverse alpha-mannosidase activities through subtle evolution of a distal substrate-binding motif. Authors: Thompson, A.J. / Spears, R.J. / Zhu, Y. / Suits, M.D.L. / Williams, S.J. / Gilbert, H.J. / Davies, G.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6f90.cif.gz | 449.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f90.ent.gz | 358.5 KB | Display | PDB format |
PDBx/mmJSON format | 6f90.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/6f90 ftp://data.pdbj.org/pub/pdb/validation_reports/f9/6f90 | HTTPS FTP |
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-Related structure data
Related structure data | 6f8zC 6f91C 6f92C 2wvyS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 82791.266 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Gene: ERS852430_04477, ERS852511_01397, SAMN02910322_03319 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): TUNER / References: UniProt: A0A174L250, UniProt: Q8A325*PLUS #2: Chemical | #3: Chemical | #4: 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: 4.23 Å3/Da / Density % sol: 70.95 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 18% (w/v) PEG 3350, 0.1 M Bis-Tris propane, pH 6.4, 0.2 M NaBr |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 2, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→49.38 Å / Num. obs: 160656 / % possible obs: 99.5 % / Redundancy: 25.1 % / Biso Wilson estimate: 40.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.195 / Rpim(I) all: 0.056 / Rrim(I) all: 0.203 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 25.9 % / Rmerge(I) obs: 2.48 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 7817 / CC1/2: 0.661 / Rpim(I) all: 0.702 / Rrim(I) all: 2.58 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2WVY Resolution: 2.4→49.38 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.923 / SU B: 7.441 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.235 / ESU R Free: 0.202 / 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: 62.755 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→49.38 Å
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Refine LS restraints |
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