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- PDB-6fku: Structure and function of aldehyde dehydrogenase from Thermus the... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6fku | ||||||
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Title | Structure and function of aldehyde dehydrogenase from Thermus thermophilus: An enzyme with an evolutionarily-distinct C-terminal arm (Recombinant protein with shortened C-terminal, in complex with NADP) | ||||||
![]() | Aldehyde dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / aldehyde dehydrogenase / Thermus thermophilus | ||||||
Function / homology | ![]() phenylacetaldehyde dehydrogenase (NAD+) activity / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / nucleotide binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hayes, K.A. / Noor, M.R. / Djeghader, A. / Soulimane, T. | ||||||
![]() | ![]() Title: The quaternary structure of Thermus thermophilus aldehyde dehydrogenase is stabilized by an evolutionary distinct C-terminal arm extension. Authors: Hayes, K. / Noor, M. / Djeghader, A. / Armshaw, P. / Pembroke, T. / Tofail, S. / Soulimane, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 218.4 KB | Display | ![]() |
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PDB format | ![]() | 172.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 39.3 KB | Display | |
Data in CIF | ![]() | 54 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6fjxC ![]() 6fk3C ![]() 6fkvC ![]() 4wj9S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 4 - 509 / Label seq-ID: 10 - 515
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 57917.590 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: TT_C0513 / Production host: ![]() ![]() |
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-Non-polymers , 7 types, 198 molecules ![](data/chem/img/PGE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/NAP.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/NAP.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PGE / #3: Chemical | #4: Chemical | ChemComp-PG4 / | #5: Chemical | #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.85 Å3/Da / Density % sol: 68.07 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 50 mM MOPS pH 7.5, 1.2 M ammonium sulfate, 1 mM NADP disodium salt |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→99.93 Å / Num. all: 1862508 / Num. obs: 70248 / % possible obs: 97.33 % / Redundancy: 26.8 % / Biso Wilson estimate: 41.0503127291 Å2 / CC1/2: 0.995 / Rrim(I) all: 0.5706 / Net I/σ(I): 6.06 |
Reflection shell | Resolution: 2.05→2.123 Å / Mean I/σ(I) obs: 0.34 / % possible all: 75.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4WJ9 Resolution: 2.4→48.11 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / SU B: 6.466 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.06 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→48.11 Å
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Refine LS restraints |
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