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Yorodumi- PDB-5az1: Crystal structure of aldo-keto reductase (AKR2E5) complexed with NADPH -
+Open data
-Basic information
Entry | Database: PDB / ID: 5az1 | ||||||
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Title | Crystal structure of aldo-keto reductase (AKR2E5) complexed with NADPH | ||||||
Components | Uncharacterized protein | ||||||
Keywords | OXIDOREDUCTASE / enzyme specificity / Lepidoptera | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bombyx mori (domestic silkworm) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Yamamoto, K. / Higashiura, A. / Suzuki, M. / Nakagawa, A. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2016 Title: Structural characterization of an aldo-keto reductase (AKR2E5) from the silkworm Bombyx mori Authors: Yamamoto, K. / Higashiura, A. / Suzuki, M. / Shiotsuki, T. / Sugahara, R. / Fujii, T. / Nakagawa, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5az1.cif.gz | 89.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5az1.ent.gz | 66.1 KB | Display | PDB format |
PDBx/mmJSON format | 5az1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/5az1 ftp://data.pdbj.org/pub/pdb/validation_reports/az/5az1 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39843.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bombyx mori (domestic silkworm) / Gene: LOC101740031 / Production host: Escherichia coli (E. coli) / References: UniProt: H9JJU9 |
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-Non-polymers , 5 types, 250 molecules
#2: Chemical | ChemComp-CA / | ||||
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#3: Chemical | ChemComp-EDO / | ||||
#4: Chemical | ChemComp-ACT / #5: Chemical | ChemComp-NDP / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.35 Å3/Da / Density % sol: 63.3 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 4 M ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: May 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→46.1 Å / Num. obs: 24781 / % possible obs: 99.7 % / Redundancy: 15.5 % / Net I/σ(I): 30 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→46.1 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.56 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.171 / 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: 35.774 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→46.1 Å
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Refine LS restraints |
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