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Yorodumi- PDB-8k2j: Crystal structure of Group 3 Oligosaccharide/Monosaccharide-relea... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8k2j | ||||||||||||
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Title | Crystal structure of Group 3 Oligosaccharide/Monosaccharide-releasing beta-N-acetylgalactosaminidase NgaDssm, apo form | ||||||||||||
Components | Oligosaccharide/Monosaccharide-releasing beta-N-acetylgalactosaminidase | ||||||||||||
Keywords | HYDROLASE / Glycoside Hydrolase | ||||||||||||
Biological species | metagenome (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å | ||||||||||||
Authors | Sumida, T. / Fushinobu, S. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: Nat Commun / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8k2j.cif.gz | 131.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8k2j.ent.gz | 99.4 KB | Display | PDB format |
PDBx/mmJSON format | 8k2j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8k2j_validation.pdf.gz | 444.4 KB | Display | wwPDB validaton report |
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Full document | 8k2j_full_validation.pdf.gz | 450.5 KB | Display | |
Data in XML | 8k2j_validation.xml.gz | 24.5 KB | Display | |
Data in CIF | 8k2j_validation.cif.gz | 37.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k2/8k2j ftp://data.pdbj.org/pub/pdb/validation_reports/k2/8k2j | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 62261.723 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli (E. coli) | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.69 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.2 M Lithium sulfate, 0.1 M Bis-Tris pH 6.0, 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: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 2, 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→47.8 Å / Num. obs: 64770 / % possible obs: 100 % / Redundancy: 23 % / CC1/2: 0.997 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.75→1.78 Å / Num. unique obs: 3512 / CC1/2: 0.688 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→47.8 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.314 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.91 Å2
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Refinement step | Cycle: 1 / Resolution: 1.76→47.8 Å
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Refine LS restraints |
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