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- PDB-7ymb: Structure of Alcohol dehydrogenase from Candida glabrata(CgADH)co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ymb | ||||||
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Title | Structure of Alcohol dehydrogenase from Candida glabrata(CgADH)complexed with NADPH | ||||||
![]() | NADPH-dependent methylglyoxal reductase GRE2 | ||||||
![]() | OXIDOREDUCTASE / ketoreducatse | ||||||
Function / homology | 3-beta hydroxysteroid dehydrogenase/isomerase / 3-beta hydroxysteroid dehydrogenase/isomerase family / 3-beta-hydroxy-delta5-steroid dehydrogenase (NAD+) activity / steroid biosynthetic process / NAD(P)-binding domain superfamily / Chem-NDP / NADPH-dependent methylglyoxal reductase GRE2![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Sun, Z.W. / Liu, Y.F. / Xu, G.C. / Ni, Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: rational desigen of CgADH from Candida glabrata for stereocomplementary reduction of azacyclone. Authors: Sun, Z.W. / Ni, Y. / Xu, G.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89.3 KB | Display | ![]() |
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PDB format | ![]() | 64.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 805.1 KB | Display | ![]() |
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Full document | ![]() | 807.2 KB | Display | |
Data in XML | ![]() | 17.5 KB | Display | |
Data in CIF | ![]() | 26.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5b6kS S: Starting model for refinement |
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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: 39062.262 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-NDP / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.75 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop Details: 0.2M Ammonium acetate, 0.1M sodium acetate pH 4.6, 30% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 150 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.54178 Å |
Detector | Type: Bruker PHOTON II / Detector: PIXEL / Date: Jul 29, 2021 / Details: multilayer |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.739→24.59 Å / Num. obs: 32695 / % possible obs: 95.05 % / Redundancy: 2.93 % / Rsym value: 0.156 / Net I/av σ(I): 66.672 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 1.85→1.89 Å / Rmerge(I) obs: 0.289 / Num. unique obs: 1678 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5B6K Resolution: 1.8→24.59 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.95 / Stereochemistry target values: ML
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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 max: 58.8 Å2 / Biso mean: 21.0281 Å2 / Biso min: 6.45 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→24.59 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11
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