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Yorodumi- PDB-6k0i: Crystal Structure of UDP-glucose 4-epimerase from Bifidobacterium... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6k0i | ||||||
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Title | Crystal Structure of UDP-glucose 4-epimerase from Bifidobacterium longum in complex with NAD+ and UDP-Glc | ||||||
Components | UDP-glucose 4-epimerase | ||||||
Keywords | ISOMERASE / Rossmann fold / HYDROLASE | ||||||
Function / homology | Function and homology information UDP-glucose 4-epimerase / UDP-glucose 4-epimerase activity / galactose catabolic process via UDP-galactose / carbohydrate metabolic process / cytosol Similarity search - Function | ||||||
Biological species | Bifidobacterium longum subsp. longum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Nam, Y.-W. / Nishimoto, M. / Arakawa, T. / Kitaoka, M. / Fushinobu, S. | ||||||
Citation | Journal: Sci Rep / Year: 2019 Title: Structural basis for broad substrate specificity of UDP-glucose 4-epimerase in the human milk oligosaccharide catabolic pathway of Bifidobacterium longum. Authors: Nam, Y.W. / Nishimoto, M. / Arakawa, T. / Kitaoka, M. / Fushinobu, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6k0i.cif.gz | 90.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k0i.ent.gz | 65 KB | Display | PDB format |
PDBx/mmJSON format | 6k0i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6k0i_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6k0i_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6k0i_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | 6k0i_validation.cif.gz | 27.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k0/6k0i ftp://data.pdbj.org/pub/pdb/validation_reports/k0/6k0i | HTTPS FTP |
-Related structure data
Related structure data | 6k0gC 6k0hC 1ek6S S: Starting model for refinement C: citing same article (ref.) |
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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: 37269.977 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bifidobacterium longum subsp. longum (strain ATCC 15707 / DSM 20219 / JCM 1217 / NCTC 11818 / E194b) (bacteria) Strain: ATCC 15707 / DSM 20219 / JCM 1217 / NCTC 11818 / E194b Gene: galE, lnpD, BLLJ_1620 / Variant: JCM 1217 / Plasmid: pET-30 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): CodonPlus (DE3)-RIL / References: UniProt: E8MF10, UDP-glucose 4-epimerase |
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#2: Chemical | ChemComp-NAD / |
#3: Chemical | ChemComp-UPG / |
#4: 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: 3.09 Å3/Da / Density % sol: 60.22 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 30% (v/v) PEG 400, 0.2 M MgCl, 0.1 M HEPES-NaOH (pH 7.5), 10 mM UDP-Glc |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 8, 2014 |
Radiation | Monochromator: Numerical link type Si(111) double crystal / 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: 44500 / % possible obs: 98.1 % / Redundancy: 18 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 37.8 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 18.2 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 7.7 / Num. unique obs: 2102 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EK6 Resolution: 1.8→36.78 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.77 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.093 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 61 Å2 / Biso mean: 17.93 Å2 / Biso min: 9.18 Å2
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Refinement step | Cycle: final / Resolution: 1.8→36.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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