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- PDB-8b5m: Crystal structure of GH47 alpha-1,2-mannosidase from Caulobacter ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8b5m | ||||||
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Title | Crystal structure of GH47 alpha-1,2-mannosidase from Caulobacter K31 strain in complex with cyclosulfamidate inhibitor | ||||||
![]() | Mannosyl-oligosaccharide 1,2-alpha-mannosidase | ||||||
![]() | HYDROLASE / Carbohydrate / Mannosidase / Inverting | ||||||
Function / homology | ![]() mannosyl-oligosaccharide 1,2-alpha-mannosidase / mannosyl-oligosaccharide 1,2-alpha-mannosidase activity / carbohydrate metabolic process / calcium ion binding / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Males, A. / Davies, G.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: GH47 and Cyclosulfamidate Authors: Males, A. / Davies, G.J. / Artola, M. / Overkleeft, H.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 203.1 KB | Display | ![]() |
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PDB format | ![]() | 154.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 813 KB | Display | ![]() |
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Full document | ![]() | 814.3 KB | Display | |
Data in XML | ![]() | 24.3 KB | Display | |
Data in CIF | ![]() | 39.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ayoS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 50520.598 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: B0SWV2, mannosyl-oligosaccharide 1,2-alpha-mannosidase | ||||
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#2: Chemical | ChemComp-5OV / ( | ||||
#3: Chemical | ChemComp-NA / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.17 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: 23% PEG3350, 0.1 M MES pH 7.0, 0.2 M ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 7, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.799 Å / Relative weight: 1 |
Reflection | Resolution: 0.97→72.07 Å / Num. obs: 230864 / % possible obs: 100 % / Redundancy: 10.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.05 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 0.97→0.99 Å / Redundancy: 10 % / Rmerge(I) obs: 1.49 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 11558 / CC1/2: 0.605 / Rpim(I) all: 0.49 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4AYO Resolution: 0.97→72.067 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.309 / SU ML: 0.016 / Cross valid method: FREE R-VALUE / ESU R: 0.02 / ESU R Free: 0.02 Details: Hydrogens have been added in their 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 / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 7.642 Å2
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Refinement step | Cycle: LAST / Resolution: 0.97→72.067 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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