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Yorodumi- PDB-2d5j: Unsaturated Glucuronyl Hydrolase Triggers Hydration of Vinyl Ethe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2d5j | ||||||
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Title | Unsaturated Glucuronyl Hydrolase Triggers Hydration of Vinyl Ether Group but not of Glycosidic Bond | ||||||
Components | unsaturated glucuronyl hydrolase | ||||||
Keywords | HYDROLASE / alpha/alpha barrel / unsaturated glucuronyl hydrolase | ||||||
Function / homology | Function and homology information gellan tetrasaccharide unsaturated glucuronosyl hydrolase / hydrolase activity, acting on glycosyl bonds / polysaccharide catabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Itoh, T. / Hashimoto, W. / Mikami, B. / Murata, K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Crystal Structure of Unsaturated Glucuronyl Hydrolase Complexed with Substrate: MOLECULAR INSIGHTS INTO ITS CATALYTIC REACTION MECHANISM 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 | 2d5j.cif.gz | 177.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d5j.ent.gz | 141.6 KB | Display | PDB format |
PDBx/mmJSON format | 2d5j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/2d5j ftp://data.pdbj.org/pub/pdb/validation_reports/d5/2d5j | 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: 42914.352 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: GL1 / 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 #2: 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: 2.33 Å3/Da / Density % sol: 47.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.6 Details: 30% PEG10000, 0.15M Tris pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Sep 27, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 93414 / % possible obs: 87.7 % / Redundancy: 4.3 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.079 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.276 / % possible all: 96.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→9.99 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1726790.34 / 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: 65.697 Å2 / ksol: 0.451516 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→9.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
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Xplor file |
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