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- PDB-6smz: Crystal structure of SLA Reductase YihU from E. Coli in complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6smz | ||||||
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Title | Crystal structure of SLA Reductase YihU from E. Coli in complex with NADH | ||||||
![]() | 3-sulfolactaldehyde reductase | ||||||
![]() | OXIDOREDUCTASE / apo / reductase / sulfoquinovose / dihydroxypropanesulfonate | ||||||
Function / homology | ![]() sulfolactaldehyde 3-reductase / 4-hydroxybutyrate dehydrogenase / 4-hydroxybutyrate dehydrogenase activity / 3-sulfolactaldehyde reductase activity / 3-hydroxyisobutyrate dehydrogenase activity / 6-sulfoquinovose(1-) catabolic process / 6-sulfoquinovose(1-) catabolic process to glycerone phosphate and 3-sulfolactaldehyde / toxin catabolic process / valine catabolic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor ...sulfolactaldehyde 3-reductase / 4-hydroxybutyrate dehydrogenase / 4-hydroxybutyrate dehydrogenase activity / 3-sulfolactaldehyde reductase activity / 3-hydroxyisobutyrate dehydrogenase activity / 6-sulfoquinovose(1-) catabolic process / 6-sulfoquinovose(1-) catabolic process to glycerone phosphate and 3-sulfolactaldehyde / toxin catabolic process / valine catabolic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding / NADP binding / protein homotetramerization / protein-containing complex / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sharma, M. / Davies, G.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Dynamic Structural Changes Accompany the Production of Dihydroxypropanesulfonate by Sulfolactaldehyde Reductase Authors: Sharma, M. / Abayakoon, P. / Lingford, J.P. / Epa, R. / John, A. / Jin, Y. / Goddard-Borger, E.D. / Davies, G.J. / Williams, S.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 241.6 KB | Display | ![]() |
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PDB format | ![]() | 193.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 49 KB | Display | |
Data in CIF | ![]() | 71.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6sm7SC ![]() 6smyC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Refine code: _
NCS ensembles :
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Components
#1: Protein | Mass: 32257.246 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: yihU, b3882, JW3853 / Plasmid: pET28a(+) / Production host: ![]() ![]() #2: Chemical | ChemComp-NAD / #3: Water | ChemComp-HOH / | 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: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: YihU was co-crystallized with 5 mM NADH using 0.2 M Ammonium acetate, 0.1 M Bis-Tris pH 6.5, 25% w/v PEG 3,350 as precipitant. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→88.95 Å / Num. obs: 119505 / % possible obs: 100 % / Redundancy: 8.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.021 / Rrim(I) all: 0.061 / Net I/σ(I): 18.8 / Num. measured all: 976872 / Scaling rejects: 165 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.473 / Num. unique obs: 5864 / CC1/2: 0.954 / Rpim(I) all: 0.172 / Rrim(I) all: 0.504 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6SM7 Resolution: 1.75→88.95 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.375 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 82.25 Å2 / Biso mean: 27.35 Å2 / Biso min: 15.58 Å2
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Refinement step | Cycle: final / Resolution: 1.75→88.95 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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