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- PDB-8k1h: Crystal structure of ethylene glycol-bound glycerol dehydrogenase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8k1h | |||||||||
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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 | ![]() | 184.7 KB | Display | ![]() |
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PDB format | ![]() | 121.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8k1gC ![]() 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
-Protein , 1 types, 1 molecules A
#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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-Non-polymers , 5 types, 260 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/TLA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/TLA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / | ||||
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#3: Chemical | ChemComp-NAD / | ||||
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.42 Å3/Da / Density % sol: 72.18 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.6 M ammonium tartrate dibasic, 0.15 M sodium acetate trihydrate(pH4.6) |
-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: Nov 27, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 40658 / % possible obs: 100 % / Redundancy: 17.6 % / Biso Wilson estimate: 29.45 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.153 / Net I/σ(I): 49.5 |
Reflection shell | Resolution: 2.1→2.14 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2023 / CC1/2: 0.88 / Rrim(I) all: 0.91 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5ZXL Resolution: 2.1→48.95 Å / SU ML: 0.1939 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.6515 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: 33.67 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→48.95 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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