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Yorodumi- PDB-5z3k: Crystal structure of glucosidase from Croceicoccus marinus at 1.8... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5z3k | ||||||
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Title | Crystal structure of glucosidase from Croceicoccus marinus at 1.8 Angstrom resolution | ||||||
Components | glucosidase | ||||||
Keywords | HYDROLASE / glycoside hydrolase / glucosidase / GH39 / Croceicoccus marinus | ||||||
Function / homology | Glycoside hydrolase, family 39 / Glycosyl hydrolases family 39 / hydrolase activity, hydrolyzing O-glycosyl compounds / Glycoside hydrolase superfamily / carbohydrate metabolic process / Uncharacterized protein Function and homology information | ||||||
Biological species | Croceicoccus marinus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.802 Å | ||||||
Authors | Shen, Y.F. / Hu, X.J. / Li, J.X. | ||||||
Citation | Journal: Front Microbiol / Year: 2019 Title: Structural and Functional Insights Into CmGH1, a Novel GH39 Family beta-Glucosidase From Deep-Sea Bacterium. Authors: Shen, Y. / Li, Z. / Huo, Y.Y. / Bao, L. / Gao, B. / Xiao, P. / Hu, X. / Xu, X.W. / Li, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5z3k.cif.gz | 216.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z3k.ent.gz | 178.7 KB | Display | PDB format |
PDBx/mmJSON format | 5z3k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5z3k_validation.pdf.gz | 440.4 KB | Display | wwPDB validaton report |
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Full document | 5z3k_full_validation.pdf.gz | 442.3 KB | Display | |
Data in XML | 5z3k_validation.xml.gz | 43.6 KB | Display | |
Data in CIF | 5z3k_validation.cif.gz | 67.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z3/5z3k ftp://data.pdbj.org/pub/pdb/validation_reports/z3/5z3k | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 54002.160 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Croceicoccus marinus (bacteria) / Gene: A9D14_15590 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1Z1FG87 #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.17 Å3/Da / Density % sol: 43.22 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.2M Ammonium acetate, 0.1M Bis-Tris pH 5.5, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 13, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→48.35 Å / Num. obs: 82629 / % possible obs: 97.3 % / Redundancy: 1.9 % / Net I/σ(I): 15.03 |
Reflection shell | Resolution: 1.8→1.86 Å |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.802→48.347 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.6 / Stereochemistry target values: ML
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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: 1.802→48.347 Å
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Refine LS restraints |
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LS refinement shell |
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