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Yorodumi- PDB-2fuz: UGL hexagonal crystal structure without glycine and DTT molecules -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fuz | ||||||
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Title | UGL hexagonal crystal structure without glycine and DTT molecules | ||||||
Components | Unsaturated glucuronyl hydrolase | ||||||
Keywords | HYDROLASE / alpha6/alpha6-barrel | ||||||
Function / homology | Function and homology information gellan tetrasaccharide unsaturated glucuronosyl hydrolase / chondroitin hydrolase activity / polysaccharide catabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Itoh, T. / Hashimoto, W. / Mikami, B. / Murata, K. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2006 Title: Substrate recognition by unsaturated glucuronyl hydrolase from Bacillus sp. GL1 Authors: Itoh, T. / Hashimoto, W. / Mikami, B. / Murata, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fuz.cif.gz | 101 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fuz.ent.gz | 77.5 KB | Display | PDB format |
PDBx/mmJSON format | 2fuz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2fuz_validation.pdf.gz | 441.9 KB | Display | wwPDB validaton report |
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Full document | 2fuz_full_validation.pdf.gz | 444.9 KB | Display | |
Data in XML | 2fuz_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | 2fuz_validation.cif.gz | 30.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fu/2fuz ftp://data.pdbj.org/pub/pdb/validation_reports/fu/2fuz | HTTPS FTP |
-Related structure data
Related structure data | 2fv0C 2fv1C 1vd5S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 42914.352 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: GL1 / Gene: ugl / Plasmid: pET3a_UGL / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q9RC92, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds | ||
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#2: Chemical | ChemComp-MPD / ( #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.97 Å3/Da / Density % sol: 68.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 50% MPD, 0.1M Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 21, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 64105 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.087 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.308 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VD5 Resolution: 1.8→15 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 589626.56 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 74.3322 Å2 / ksol: 0.357016 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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