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Yorodumi- PDB-5evo: Structure of Dehydroascrobate Reductase from Pennisetum Americanu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5evo | ||||||
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Title | Structure of Dehydroascrobate Reductase from Pennisetum Americanum in complex with two non-native ligands, Acetate in the G-site and Glycerol in the H-site | ||||||
Components | Dehydroascorbate reductase | ||||||
Keywords | OXIDOREDUCTASE / APO(NATIVE) / DHAR / Non-Native ligands / Acetate (G-site) / Glycerol (H-site) | ||||||
Function / homology | Function and homology information ascorbate glutathione cycle / glutathione dehydrogenase (ascorbate) / glutathione dehydrogenase (ascorbate) activity / glutathione transferase activity Similarity search - Function | ||||||
Biological species | Cenchrus americanus (bulrush millet) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.51 Å | ||||||
Authors | Kumar, A.O. / Das, B.K. / Arockiasamy, A. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2016 Title: Non-native ligands define the active site of Pennisetum glaucum (L.) R. Br dehydroascorbate reductase. Authors: Krishna Das, B. / Kumar, A. / Maindola, P. / Mahanty, S. / Jain, S.K. / Reddy, M.K. / Arockiasamy, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5evo.cif.gz | 55.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5evo.ent.gz | 39.6 KB | Display | PDB format |
PDBx/mmJSON format | 5evo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5evo_validation.pdf.gz | 441 KB | Display | wwPDB validaton report |
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Full document | 5evo_full_validation.pdf.gz | 441.8 KB | Display | |
Data in XML | 5evo_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 5evo_validation.cif.gz | 13.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ev/5evo ftp://data.pdbj.org/pub/pdb/validation_reports/ev/5evo | HTTPS FTP |
-Related structure data
Related structure data | 5iqyC 5evn 5evp 5evq 5evr 5evs 5evt 5evu 5evv 5evw 5evx C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23726.203 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cenchrus americanus (bulrush millet) / Production host: Escherichia coli (E. coli) References: UniProt: U5XYA0, glutathione dehydrogenase (ascorbate) |
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#2: Chemical | ChemComp-ACT / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: SODIUM ACETATE, AMMONIUM SULFATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 18, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 9893 / % possible obs: 99.4 % / Redundancy: 8.8 % / Biso Wilson estimate: 62.74 Å2 / Net I/σ(I): 28.99 |
-Processing
Software |
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Refinement | Resolution: 2.51→49.14 Å / Cor.coef. Fo:Fc: 0.9376 / Cor.coef. Fo:Fc free: 0.9103 / SU R Cruickshank DPI: 0.371 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.417 / SU Rfree Blow DPI: 0.257 / SU Rfree Cruickshank DPI: 0.252
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Displacement parameters | Biso mean: 52.89 Å2
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Refine analyze | Luzzati coordinate error obs: 0.316 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.51→49.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.51→2.81 Å / Total num. of bins used: 5
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