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Yorodumi- PDB-8k2f: Crystal structure of Group 1 oligosaccharide-releasing beta-N-ace... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8k2f | ||||||||||||
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Title | Crystal structure of Group 1 oligosaccharide-releasing beta-N-acetylgalactosaminidase NgaCa from Cohnella abietis, apo 1 form | ||||||||||||
Components | Oligosaccharide-releasing beta-N-acetylgalactosaminidase | ||||||||||||
Keywords | HYDROLASE / Glycoside hydrolase | ||||||||||||
Function / homology | Glycoside hydrolase 123, C-terminal / Glycoside hydrolase 123, catalytic domain / Glycoside hydrolase 123 catalytic domain-containing protein Function and homology information | ||||||||||||
Biological species | Cohnella abietis (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 | 8k2f.cif.gz | 119.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8k2f.ent.gz | 88.7 KB | Display | PDB format |
PDBx/mmJSON format | 8k2f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8k2f_validation.pdf.gz | 433.9 KB | Display | wwPDB validaton report |
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Full document | 8k2f_full_validation.pdf.gz | 435.8 KB | Display | |
Data in XML | 8k2f_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | 8k2f_validation.cif.gz | 31.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k2/8k2f ftp://data.pdbj.org/pub/pdb/validation_reports/k2/8k2f | HTTPS FTP |
-Related structure data
Related structure data | 8k2gC 8k2hC 8k2iC 8k2jC 8k2kC 8k2lC 8k2mC 8k2nC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 58137.711 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cohnella abietis (bacteria) / Gene: KCTCHS21_21730 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3T1D3V8 |
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#2: Chemical | ChemComp-MG / |
#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: 2.08 Å3/Da / Density % sol: 40.86 % |
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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: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
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→49.88 Å / Num. obs: 47285 / % possible obs: 98.4 % / Redundancy: 7.2 % / CC1/2: 0.993 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 1.75→1.78 Å / Num. unique obs: 2505 / CC1/2: 0.942 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→49.88 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.246 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.118 / 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: 21.746 Å2
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Refinement step | Cycle: 1 / Resolution: 1.75→49.88 Å
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Refine LS restraints |
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