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- PDB-3rud: Alternative analogs as viable substrates of UDP-hexose 4-epimerases -
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Open data
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Basic information
Entry | Database: PDB / ID: 3rud | ||||||
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Title | Alternative analogs as viable substrates of UDP-hexose 4-epimerases | ||||||
![]() | WbgU | ||||||
![]() | ISOMERASE / Rossmann fold / UDP-hexose 4-epimerase | ||||||
Function / homology | ![]() UDP-N-acetylglucosamine 4-epimerase / UDP-N-acetylglucosamine 4-epimerase activity / O antigen biosynthetic process / nucleotide binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bhatt, V.S. / Guan, W. / Wang, P.G. | ||||||
![]() | ![]() Title: Alternative analogs as viable substrates of UDP-hexose 4-epimerases Authors: Bhatt, V.S. / Guan, W. / Wang, P.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 283.1 KB | Display | ![]() |
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PDB format | ![]() | 229.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 52.1 KB | Display | |
Data in CIF | ![]() | 71.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3rueC ![]() 3rufC ![]() 3ruhC ![]() 3lu1S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 39822.109 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-UNL / Num. of mol.: 4 / Source method: obtained synthetically #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.61 % |
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Crystal grow | Temperature: 298.15 K / Method: microbatch under oil / pH: 6.5 Details: 25% PEG 3350, 0.2 M Ammonium Sulfate, 200 mM Bis Tris Propane pH 6.5, microbatch under oil, temperature 298.15K |
-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 6, 2011 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→75.9 Å / Num. all: 64466 / Num. obs: 64466 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 3LU1 Resolution: 2.3→74.94 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.918 / SU B: 6.932 / SU ML: 0.174 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.231 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→74.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.302→2.362 Å / Total num. of bins used: 20
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