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- PDB-8sxy: X-ray crystal structure of UDP- 2,3-diacetamido-2,3-dideoxy-glucu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8sxy | ||||||
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Title | X-ray crystal structure of UDP- 2,3-diacetamido-2,3-dideoxy-glucuronic acid-2-epimerase from Thermus thermophilus strain HB27 in complex with its product UDP-2,3-diacetamido-2,3-dideoxy-d-mannuronic acid at pH 5 | ||||||
![]() | UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid-2-epimerase | ||||||
![]() | ISOMERASE / lipopolysaccharide / O-antigen / 2-epimerase | ||||||
Function / homology | UDP-N-acetylglucosamine 2-epimerase (non-hydrolysing) / UDP-N-acetylglucosamine 2-epimerase WecB-like / UDP-N-acetylglucosamine 2-epimerase domain / UDP-N-acetylglucosamine 2-epimerase / UDP-N-acetylglucosamine 2-epimerase activity / nucleotide binding / Chem-MJ3 / UDP-N-acetylglucosamine 2-epimerase![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | McKnight, J.O. / Thoden, J.B. / Holden, H.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural analysis of a bacterial UDP-sugar 2-epimerase reveals the active site architecture before and after catalysis. Authors: Thoden, J.B. / McKnight, J.O. / Kroft, C.W. / Jast, J.D.T. / Holden, H.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 169.4 KB | Display | ![]() |
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PDB format | ![]() | 131 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8sxvC ![]() 8sxwC ![]() 8sy0C ![]() 8sy9C ![]() 8syaC ![]() 8sybC ![]() 8sydC ![]() 8syeC ![]() 8syhC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 41995.070 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: Protein incubated with 5 mM UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid. Precipitant solution: 22-27% pentaerythritol propoxylate (5/4 PO/OH), 100 mM homopipes (pH 5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å |
Detector | Type: Bruker PHOTON II / Detector: PIXEL / Date: Dec 16, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 71545 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rsym value: 0.056 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 3.5 / Num. unique obs: 10677 / Rsym value: 0.3 / % possible all: 98.7 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.549 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→41.71 Å
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Refine LS restraints |
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