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Yorodumi- PDB-6f92: Structure of the family GH92 alpha-mannosidase BT3965 from Bacter... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6f92 | |||||||||
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Title | Structure of the family GH92 alpha-mannosidase BT3965 from Bacteroides thetaiotaomicron in complex with Mannoimidazole (ManI) | |||||||||
Components | Putative alpha-1,2-mannosidase | |||||||||
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: 1.9 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 | 6f92.cif.gz | 657.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f92.ent.gz | 533.7 KB | Display | PDB format |
PDBx/mmJSON format | 6f92.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/6f92 ftp://data.pdbj.org/pub/pdb/validation_reports/f9/6f92 | HTTPS FTP |
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-Related structure data
Related structure data | 6f8zC 6f90C 6f91C 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / Refine code: 0
NCS ensembles :
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 87566.141 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Gene: HMPREF2534_04919 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): TUNER / References: UniProt: A0A139JT15, UniProt: Q8A0Q6*PLUS |
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-Non-polymers , 7 types, 2327 molecules
#2: Chemical | ChemComp-NA / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-MVL / ( #6: Chemical | ChemComp-EDO / #7: Chemical | #8: 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: 2.13 Å3/Da / Density % sol: 42.28 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20% w/v PEG 3350, 0.2 M NaNO3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 11, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→46.73 Å / Num. obs: 216402 / % possible obs: 96.1 % / Redundancy: 4.4 % / Biso Wilson estimate: 14.7 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.129 / Rrim(I) all: 0.203 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.941 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 10727 / CC1/2: 0.506 / Rpim(I) all: 0.785 / Rrim(I) all: 1.229 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2WVY Resolution: 1.9→46.73 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.509 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.147 / 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: 23.019 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→46.73 Å
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Refine LS restraints |
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