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- PDB-6k0g: 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: 6k0g | ||||||
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Title | Crystal Structure of UDP-glucose 4-epimerase from Bifidobacterium longum in complex with NAD+ and UDP | ||||||
![]() | UDP-glucose 4-epimerase | ||||||
![]() | ISOMERASE / Rossmann fold | ||||||
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 | ![]() | 92.7 KB | Display | ![]() |
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PDB format | ![]() | 66.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 18.2 KB | Display | |
Data in CIF | ![]() | 28.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6k0hC ![]() 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
#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: lnpD, BLLJ_1620 / Variant: JCM 1217 / Plasmid: pET-30 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-UDP / |
#3: Chemical | ChemComp-NAD / |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.83 % |
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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 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 5, 2013 |
Radiation | Monochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 44804 / % possible obs: 100 % / Redundancy: 18.1 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 31.8 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 20.6 % / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 6.7 / Num. unique obs: 2104 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1EK6 Resolution: 1.8→40.17 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.697 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.088 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: 72.58 Å2 / Biso mean: 21.326 Å2 / Biso min: 6.63 Å2
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Refinement step | Cycle: final / Resolution: 1.8→40.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.801→1.848 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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