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Open data
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Basic information
Entry | Database: PDB / ID: 7bu2 | ||||||
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Title | Structure of alcohol dehydrogenase YjgB from Escherichia coli | ||||||
![]() | Alcohol dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / Alcohol Dehydrogenase | ||||||
Function / homology | ![]() alcohol dehydrogenase (NADP+) / alcohol dehydrogenase (NADP+) activity / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / fatty acid metabolic process / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nguyen, G.T. / Kim, Y.-G. / Ahn, J.-W. / Chang, J.H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Basis for Broad Substrate Selectivity of Alcohol Dehydrogenase YjgB from Escherichia coli . Authors: Nguyen, G.T. / Kim, Y.G. / Ahn, J.W. / Chang, J.H. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 165.2 KB | Display | ![]() |
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PDB format | ![]() | 128.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7bu3C ![]() 1yqdS S: Starting model for refinement C: citing same article ( |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 37568.875 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: yjgB, ahr, AC789_1c46870, AM446_24685, AM464_15880, AUQ13_10955, AWP75_26740, BE963_12920, BON76_03580, BON87_21450, BvCms2454_04261, BvCmsKKP061_04826, BvCmsKSP011_04570, BvCmsKSP024_01161, ...Gene: yjgB, ahr, AC789_1c46870, AM446_24685, AM464_15880, AUQ13_10955, AWP75_26740, BE963_12920, BON76_03580, BON87_21450, BvCms2454_04261, BvCmsKKP061_04826, BvCmsKSP011_04570, BvCmsKSP024_01161, BvCmsKSP045_03147, BvCmsKSP067_02166, BvCmsNSP047_01920, CRX46_16815, D9J60_11645, DJ503_08680, DS732_03420, EC3234A_79c00790, ERS085365_04790, ERS085374_04180, ERS085416_04717, ERS139211_04850, EYY27_20520, F0312_23505, F1E03_04805, FNJ69_20595, NCTC8959_04532, NCTC9050_02355, NCTC9077_05531, NCTC9117_05474, PGD_03453, SAMEA3472056_04737, WR15_06500, YDC107_2991 Production host: ![]() ![]() References: UniProt: A0A024L8S1, UniProt: P27250*PLUS, alcohol dehydrogenase (NADP+) #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-ZN / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tris-HCl, pH 7.0, and 16% (w/v) PEG 3350 with 0.2 M Lithium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 14, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. obs: 95566 / % possible obs: 100 % / Redundancy: 7.4 % / CC1/2: 0.97465 / Net I/σ(I): 36.2 |
Reflection shell | Resolution: 1.55→1.58 Å / Num. unique obs: 4760 / CC1/2: 0.894 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1YQD Resolution: 1.553→25.015 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.53
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.42 Å2 / Biso mean: 23.8661 Å2 / Biso min: 9.71 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.553→25.015 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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