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Open data
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Basic information
Entry | Database: PDB / ID: 8xr3 | ||||||
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Title | Crystal structure of AKRtyl-apo2 | ||||||
![]() | Aldo/keto reductase | ||||||
![]() | OXIDOREDUCTASE / apo structure / Aldo-keto reductase | ||||||
Function / homology | NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / cytosol / Aldo/keto reductase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lin, S. / Dai, S. / Xiao, Z. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A three-level regulatory mechanism of the aldo-keto reductase subfamily AKR12D. Authors: Xiao, Z. / Zha, J. / Yang, X. / Huang, T. / Huang, S. / Liu, Q. / Wang, X. / Zhong, J. / Zheng, J. / Liang, R. / Deng, Z. / Zhang, J. / Lin, S. / Dai, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 140.5 KB | Display | ![]() |
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PDB format | ![]() | 107.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434 KB | Display | ![]() |
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Full document | ![]() | 437.3 KB | Display | |
Data in XML | ![]() | 26 KB | Display | |
Data in CIF | ![]() | 37.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8jwkC ![]() 8jwlC ![]() 8jwmC ![]() 8jwnC ![]() 8jwoC ![]() 8xr2C ![]() 8xr4C 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36293.703 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.61 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 10 % w/v PEG 4000, 10 % v/v 2-Propanol, 0.1 M Sodium HEPES, pH 7.0 |
-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: Dec 3, 2023 |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97862 Å / Relative weight: 1 |
Reflection | Resolution: 2.31→86.39 Å / Num. obs: 36443 / % possible obs: 100 % / Redundancy: 13.3 % / Biso Wilson estimate: 31.93 Å2 / CC1/2: 0.997 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.31→2.43 Å / Num. unique obs: 5300 / CC1/2: 0.833 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 39.44 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.31→38.65 Å
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Refine LS restraints |
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LS refinement shell |
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