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- PDB-8k2g: Crystal structure of Group 1 Oligosaccharide-releasing beta-N-ace... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8k2g | ||||||||||||
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Title | Crystal structure of Group 1 Oligosaccharide-releasing beta-N-acetylgalactosaminidase NgaCa from Cohnella abietis, apo 2 form | ||||||||||||
![]() | Oligosaccharide-releasing beta-N-acetylgalactosaminidase | ||||||||||||
![]() | HYDROLASE / Glycoside hydrolase | ||||||||||||
Function / homology | Glycoside hydrolase 123, C-terminal / Glycoside hydrolase 123, catalytic domain / Glycoside hydrolase 123 catalytic domain-containing protein![]() | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Sumida, T. / Fushinobu, S. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Genetic and functional diversity of beta-N-acetylgalactosamine-targeting glycosidases expanded by deep-sea metagenome analysis. Authors: Sumida, T. / Hiraoka, S. / Usui, K. / Ishiwata, A. / Sengoku, T. / Stubbs, K.A. / Tanaka, K. / Deguchi, S. / Fushinobu, S. / Nunoura, T. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 227.4 KB | Display | ![]() |
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PDB format | ![]() | 178.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.6 KB | Display | ![]() |
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Full document | ![]() | 442.2 KB | Display | |
Data in XML | ![]() | 41.9 KB | Display | |
Data in CIF | ![]() | 62.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8k2fC ![]() 8k2hC ![]() 8k2iC ![]() 8k2jC ![]() 8k2kC ![]() 8k2lC ![]() 8k2mC ![]() 8k2nC C: citing same article ( |
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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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 58137.711 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.62 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M Bis-Tris pH 6.5, 25% w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 17, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→48.36 Å / Num. obs: 96240 / % possible obs: 97.1 % / Redundancy: 3.5 % / CC1/2: 0.963 / Rmerge(I) obs: 0.093 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 1.75→1.78 Å / Num. unique obs: 4648 / CC1/2: 0.872 |
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Processing
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Refinement | Method to determine structure: ![]()
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.853 Å2
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Refinement step | Cycle: 1 / Resolution: 1.75→47.67 Å
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Refine LS restraints |
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