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- PDB-7r5t: CRYSTAL STRUCTURE OF E.coli ALCOHOL DEHYDROGENASE - FucO MUTANT F... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7r5t | ||||||
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Title | CRYSTAL STRUCTURE OF E.coli ALCOHOL DEHYDROGENASE - FucO MUTANT F254I COMPLEXED WITH FE, NADH, AND GLYCEROL | ||||||
![]() | 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. / 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 | ![]() | 303.4 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.7 MB | Display | ![]() |
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Full document | ![]() | 3.7 MB | Display | |
Data in XML | ![]() | 30.3 KB | Display | |
Data in CIF | ![]() | 42.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7qnfC ![]() 7qniC ![]() 7qnjC ![]() 7r0pC ![]() 7r3dC ![]() 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: 41531.320 Da / Num. of mol.: 2 / Mutation: F254I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: fucO, Z4116, ECs3659 Production host: ![]() ![]() Strain (production host): XL1-Blue / References: UniProt: P0A9S2, lactaldehyde reductase |
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-Non-polymers , 5 types, 253 molecules ![](data/chem/img/NAI.gif)
![](data/chem/img/APR.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/APR.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / #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: 2.28 Å3/Da / Density % sol: 46.07 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2M Magnesium chloride hexahydrate; 0.1M Bis-Tris, pH 5.5; 25% w/v PEG 3350 |
-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: May 11, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→61.841 Å / Num. obs: 64213 / % possible obs: 99.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 19.5 Å2 / CC1/2: 0.993 / Rpim(I) all: 0.056 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 1.85→1.89 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3986 / CC1/2: 0.85 / Rpim(I) all: 0.273 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1RRM Resolution: 1.85→61.841 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.725 / SU ML: 0.108 / Cross valid method: FREE R-VALUE / ESU R: 0.141 / ESU R Free: 0.129 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: 26.386 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→61.841 Å
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Refine LS restraints |
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LS refinement shell |
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