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Open data
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Basic information
Entry | Database: PDB / ID: 7xpo | ||||||
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Title | Crystal Structure of UDP-Glc/GlcNAc 4-Epimerase with NAD/UDP-Glc | ||||||
![]() | UDP-glucose 4-epimerase | ||||||
![]() | PLANT PROTEIN / Epimerase / Complex / NAD / UDP-Glc | ||||||
Function / homology | ![]() Isomerases; Racemases and epimerases; Acting on carbohydrates and derivatives / UDP-glucose 4-epimerase activity / galactose catabolic process via UDP-galactose / rRNA processing / nucleotide binding / RNA binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, Y.H. / Wang, X.C. / Zhang, C.R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A maize epimerase modulates cell wall synthesis and glycosylation during stomatal morphogenesis. Authors: Zhou, Y. / Zhang, T. / Wang, X. / Wu, W. / Xing, J. / Li, Z. / Qiao, X. / Zhang, C. / Wang, X. / Wang, G. / Li, W. / Bai, S. / Li, Z. / Suo, Y. / Wang, J. / Niu, Y. / Zhang, J. / Lan, C. / ...Authors: Zhou, Y. / Zhang, T. / Wang, X. / Wu, W. / Xing, J. / Li, Z. / Qiao, X. / Zhang, C. / Wang, X. / Wang, G. / Li, W. / Bai, S. / Li, Z. / Suo, Y. / Wang, J. / Niu, Y. / Zhang, J. / Lan, C. / Hu, Z. / Li, B. / Zhang, X. / Wang, W. / Galbraith, D.W. / Chen, Y. / Guo, S. / Song, C.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 294.5 KB | Display | ![]() |
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PDB format | ![]() | 235.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 35.4 KB | Display | |
Data in CIF | ![]() | 53.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7xppC ![]() 7xpqC ![]() 1hzjS S: Starting model for refinement 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: 38965.469 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: C0HI30, Isomerases; Racemases and epimerases; Acting on carbohydrates and derivatives #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: 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: 2.3 Å3/Da / Density % sol: 46.43 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop / Details: 0.1M Sodium malonate pH 5.0, 12% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 7, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→27.224 Å / Num. obs: 191996 / % possible obs: 98.93 % / Redundancy: 6.6 % / CC1/2: 0.999 / Net I/σ(I): 15.81 |
Reflection shell | Resolution: 1.25→1.295 Å / Num. unique obs: 18989 / CC1/2: 0.664 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1HZJ Resolution: 1.25→27.224 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.06 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.82 Å2 / Biso mean: 18.9068 Å2 / Biso min: 9.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.25→27.224 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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