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Open data
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Basic information
Entry | Database: PDB / ID: 1iy8 | ||||||
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Title | Crystal Structure of Levodione Reductase | ||||||
![]() | LEVODIONE REDUCTASE | ||||||
![]() | OXIDOREDUCTASE | ||||||
Function / homology | ![]() Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sogabe, S. / Fukami, T. / Shiratori, Y. / Yoshizumi, A. / Wada, M. | ||||||
![]() | ![]() Title: The Crystal Structure and Stereospecificity of Levodione Reductase from Corynebacterium aquaticum M-13 Authors: Sogabe, S. / Yoshizumi, A. / Fukami, T. / Shiratori, Y. / Shimizu, S. / Takagi, H. / Nakamori, S. / Wada, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 402.1 KB | Display | ![]() |
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PDB format | ![]() | 328.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.6 MB | Display | ![]() |
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Full document | ![]() | 2.6 MB | Display | |
Data in XML | ![]() | 81.1 KB | Display | |
Data in CIF | ![]() | 108.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2hsdS S: Starting model for refinement |
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Similar structure data |
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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: 27945.305 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-MRD / ( #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.35 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG MME 2000, magnesium chloride, MPD, glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 15 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.6→40 Å / Num. obs: 261092 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 | |||||||||||||||
Reflection shell | Resolution: 1.6→1.7 Å / % possible all: 83.2 | |||||||||||||||
Reflection | *PLUS Lowest resolution: 50 Å / % possible obs: 92.1 % / Redundancy: 4 % / Num. measured all: 1031771 / Rmerge(I) obs: 0.081 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 82.7 % / Rmerge(I) obs: 0.263 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2HSD Resolution: 1.6→40 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati coordinate error obs: 0.18 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.1 Å | ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→40 Å
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Refine LS restraints |
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Refinement | *PLUS Num. reflection obs: 16602 / % reflection Rfree: 5 % / Rfactor Rfree: 0.218 | ||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.534 | ||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 1.7 Å / Rfactor Rfree: 0.281 / Rfactor Rwork: 0.254 |