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- PDB-6k0h: Crystal Structure of UDP-glucose 4-epimerase from Bifidobacterium... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6k0h | ||||||
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Title | Crystal Structure of UDP-glucose 4-epimerase from Bifidobacterium longum in complex with NAD+ and UDP-GlcNAc | ||||||
![]() | UDP-glucose 4-epimerase | ||||||
![]() | ISOMERASE / Rossmann fold / HYDROLASE | ||||||
Function / homology | ![]() UDP-glucose 4-epimerase / UDP-glucose 4-epimerase activity / galactose catabolic process via UDP-galactose / carbohydrate metabolic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nam, Y.-W. / Nishimoto, M. / Arakawa, T. / Kitaoka, M. / Fushinobu, S. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 90.5 KB | Display | ![]() |
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PDB format | ![]() | 64.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 17.1 KB | Display | |
Data in CIF | ![]() | 24.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6k0gC ![]() 6k0iC ![]() 1ek6S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 38341.117 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 15707 / DSM 20219 / JCM 1217 / NCTC 11818 / E194b Gene: galE, lnpD, BLLJ_1620 / Variant: JCM 1217 / Plasmid: pET-30 / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 217 molecules ![](data/chem/img/PEG.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/UD1.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/UD1.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-NAD / | #4: Chemical | ChemComp-UD1 / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.1 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 30% (v/v) PEG400, 0.2 M MgCl, 0.1 M HEPES-NaOH (pH 7.5), and 10 mM UDP-GlcNAc |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 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: 2→50 Å / Num. obs: 32699 / % possible obs: 100 % / Redundancy: 16.9 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 28.2 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 17 % / Rmerge(I) obs: 0.951 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 1585 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1EK6 Resolution: 2→34.75 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.138 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: 87.59 Å2 / Biso mean: 33.788 Å2 / Biso min: 13.62 Å2
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Refinement step | Cycle: final / Resolution: 2→34.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.996→2.048 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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