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Yorodumi- PDB-8wop: Crystal structure of Arabidopsis thaliana UDP-glucose 4-epimerase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8wop | ||||||||||||
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Title | Crystal structure of Arabidopsis thaliana UDP-glucose 4-epimerase 2 (AtUGE2) complexed with UDP, wild-type | ||||||||||||
Components | UDP-glucose 4-epimerase 2 | ||||||||||||
Keywords | ISOMERASE | ||||||||||||
Function / homology | Function and homology information salicylic acid binding / UDP-glucose 4-epimerase / UDP-glucose 4-epimerase activity / cell wall biogenesis / galactose metabolic process / cell wall organization / cytosol Similarity search - Function | ||||||||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||||||||
Authors | Matsumoto, M. / Umezawa, A. / Kotake, T. / Fushinobu, S. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: Plant J. / Year: 2024 Title: Cytosolic UDP-L-arabinose synthesis by bifunctional UDP-glucose 4-epimerases in Arabidopsis. Authors: Umezawa, A. / Matsumoto, M. / Handa, H. / Nakazawa, K. / Miyagawa, M. / Seifert, G.J. / Takahashi, D. / Fushinobu, S. / Kotake, T. #1: Journal: Biochem J / Year: 2009 Title: Bifunctional cytosolic UDP-glucose 4-epimerases catalyse the interconversion between UDP-D-xylose and UDP-L-arabinose in plants. Authors: Kotake, T. / Takata, R. / Verma, R. / Takaba, M. / Yamaguchi, D. / Orita, T. / Kaneko, S. / Matsuoka, K. / Koyama, T. / Reiter, W.D. / Tsumuraya, Y. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8wop.cif.gz | 147.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8wop.ent.gz | 113.6 KB | Display | PDB format |
PDBx/mmJSON format | 8wop.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wo/8wop ftp://data.pdbj.org/pub/pdb/validation_reports/wo/8wop | HTTPS FTP |
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-Related structure data
Related structure data | 8wovC 8wowC 1ek6S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 40598.730 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: UGE2,At4g23920 / Plasmid: pET-15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-Gold(DE3) / References: UniProt: Q9T0A7 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.52 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20-22% (w/v) PEG3350 and 0.16-0.18 M magnesium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 13, 2022 |
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: 2.35→48.23 Å / Num. obs: 28665 / % possible obs: 99.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 29.5 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.062 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.569 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 2785 / CC1/2: 0.728 / Rpim(I) all: 0.374 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EK6 Resolution: 2.35→48.23 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.921 / SU B: 9.3 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.419 / ESU R Free: 0.252 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.142 Å2
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Refinement step | Cycle: 1 / Resolution: 2.35→48.23 Å
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Refine LS restraints |
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