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- PDB-7qnf: CRYSTAL STRUCTURE OF E.coli ALCOHOL DEHYDROGENASE - FucO MUTANT N... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7qnf | ||||||
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Title | CRYSTAL STRUCTURE OF E.coli ALCOHOL DEHYDROGENASE - FucO MUTANT N151G, L259V COMPLEXED WITH FE, NAD+, AND ETHYLENE GLYCOL | ||||||
![]() | Lactaldehyde reductase | ||||||
![]() | OXIDOREDUCTASE / FucO / NADH / Dehydrogenase / aldehyde reductase | ||||||
Function / homology | ![]() lactaldehyde reductase / R-lactaldehyde reductase activity / S-lactaldehyde reductase activity / fucose catabolic process / alcohol dehydrogenase (NAD+) activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sridhar, S. / Kiema, T.R. / Wierenga, R.K. / Widersten, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of lactaldehyde reductase, FucO, link enzyme activity to hydrogen bond networks and conformational dynamics. Authors: Zavarise, A. / Sridhar, S. / Kiema, T.R. / Wierenga, R.K. / Widersten, 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 | ![]() | 530.7 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 481 KB | Display | ![]() |
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Full document | ![]() | 487 KB | Display | |
Data in XML | ![]() | 29.8 KB | Display | |
Data in CIF | ![]() | 42.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7qniC ![]() 7qnjC ![]() 7r0pC ![]() 7r3dC ![]() 7r5tC ![]() 1rrmS 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, 2 molecules AAABBB
#1: Protein | Mass: 41464.230 Da / Num. of mol.: 2 / Mutation: N151G,L259V,S315G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: fucO, Z4116, ECs3659 / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 279 molecules ![](data/chem/img/FE.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/APR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/APR.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.67 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Bis-tris pH 8.5, 20 % (w/v) PEG 6000, 0.2 M NaF |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Aug 6, 2019 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→36.71 Å / Num. obs: 40916 / % possible obs: 100 % / Redundancy: 13.3 % / Biso Wilson estimate: 32.565 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.07 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.14→2.2 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3299 / CC1/2: 0.522 / Rpim(I) all: 0.976 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1RRM Resolution: 2.14→36.707 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.944 / Cross valid method: FREE R-VALUE / ESU R: 0.252 / ESU R Free: 0.194 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.637 Å2
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Refinement step | Cycle: LAST / Resolution: 2.14→36.707 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 |
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