+Open data
-Basic information
Entry | Database: PDB / ID: 5c0q | ||||||
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Title | Crystal structure of Zn bound CbsA from Thermotoga neapolitana | ||||||
Components | Beta-N-acetylhexosaminidaseHexosaminidase | ||||||
Keywords | HYDROLASE / cbsA / Thermotoga / thermostable enzyme / beta-N-acetylglucosaminidase | ||||||
Function / homology | Function and homology information hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Thermotoga neapolitana (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.499 Å | ||||||
Authors | Ha, N.C. / Kim, J.S. / Yoon, B.Y. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2015 Title: Crystal structure of beta-N-acetylglucosaminidase CbsA from Thermotoga neapolitana Authors: Kim, J.S. / Yoon, B.Y. / Ahn, J. / Cha, J. / Ha, N.C. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2012 Title: Crystallization and preliminary X-ray crystallographic analysis of the beta-N-acetylglucosaminidase CbsA from Thermotoga neapolitana Authors: Yoon, B.Y. / Jiao, L. / Moon, H.R. / Cha, J. / Ha, N.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5c0q.cif.gz | 351.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5c0q.ent.gz | 296.9 KB | Display | PDB format |
PDBx/mmJSON format | 5c0q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c0/5c0q ftp://data.pdbj.org/pub/pdb/validation_reports/c0/5c0q | HTTPS FTP |
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-Related structure data
-Links
-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: 52637.305 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga neapolitana (bacteria) / Gene: cbsA / Production host: Escherichia coli (E. coli) / References: UniProt: Q9AG27, beta-N-acetylhexosaminidase #2: Chemical | ChemComp-ZN / |
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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: 3 Å3/Da / Density % sol: 59.02 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop Details: 0.1 M HEPES pH 7.5, 1.0 M sodium acetate, 0.05 M CdCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.28248 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 23, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28248 Å / Relative weight: 1 |
Reflection | Resolution: 2.499→20 Å / Num. obs: 169006 / % possible obs: 99.8 % / Redundancy: 8.4 % / Net I/σ(I): 31 |
-Processing
Software |
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Refinement | Resolution: 2.499→19.966 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.52 / Phase error: 24.19 / Stereochemistry target values: ML Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.499→19.966 Å
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Refine LS restraints |
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LS refinement shell |
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