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- PDB-8k1g: Crystal structure of ethylene glycol-bound glycerol dehydrogenase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8k1g | |||||||||
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Title | Crystal structure of ethylene glycol-bound glycerol dehydrogenase from Klebsiella pneumoniae | |||||||||
![]() | Glycerol dehydrogenase | |||||||||
![]() | OXIDOREDUCTASE / Glycerol Dehydrogenase / Ethylene Glycol | |||||||||
Function / homology | ![]() glycerol dehydrogenase / oxidoreductase activity, acting on CH-OH group of donors / glycerol metabolic process / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kang, W. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structure of Glycerol Dehydrogenase from Klebsiella pneumoniae Authors: Ko, G.S. / Nguyen, T.Q. / Kho, S. / Kang, W. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 178.2 KB | Display | ![]() |
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PDB format | ![]() | 118.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.5 MB | Display | ![]() |
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Full document | ![]() | 2.5 MB | Display | |
Data in XML | ![]() | 16.6 KB | Display | |
Data in CIF | ![]() | 23.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8k1hC ![]() 5zxlS S: Starting model for refinement 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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Unit cell |
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Components
#1: Protein | Mass: 38784.152 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | ChemComp-ZN / | ||||||
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.31 Å3/Da / Density % sol: 71.45 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.6 M ammonium tartrate dibasic, 0.15 M sodium acetate tribasic |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: 0 / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 24, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97942 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→50 Å / Num. obs: 40012 / % possible obs: 100 % / Redundancy: 17.9 % / Biso Wilson estimate: 31.02 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.153 / Net I/σ(I): 19 |
Reflection shell | Resolution: 2.09→2.14 Å / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1977 / CC1/2: 0.935 / Rrim(I) all: 0.934 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5ZXL Resolution: 2.09→48.5 Å / SU ML: 0.2092 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.5518 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: 34.1 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.09→48.5 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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