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- PDB-8yu6: The structure of thiocyanate dehydrogenase mutant with the H447Q ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8yu6 | ||||||
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Title | The structure of thiocyanate dehydrogenase mutant with the H447Q substitution from Pelomicrobium methylotrophicum (pmTcDH H447Q), activated by crystal soaking with 1mM CuCl2 and 1 mM sodium ascorbate | ||||||
![]() | Twin-arginine translocation signal domain-containing protein | ||||||
![]() | OXIDOREDUCTASE / Thiocyanate dehydrogenase / Point mutation in the active center / pmTcDH H447Q / Trinuclear copper center / Pelomicrobium methylotrophicum / Cu(I) activation in crystal | ||||||
Function / homology | Nitrous oxide reductase, N-terminal / Quinoprotein amine dehydrogenase, beta chain-like / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / WD40/YVTN repeat-like-containing domain superfamily / metal ion binding / COPPER (II) ION / Twin-arginine translocation signal domain-containing protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Varfolomeeva, L.A. / Shipkov, N.S. / Dergousova, N.I. / Boyko, K.M. / Tikhonova, T.V. / Popov, V.O. | ||||||
Funding support | 1items
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![]() | ![]() Title: The structure of thiocyanate dehydrogenase mutant with the H447Q substitution from Pelomicrobium methylotrophicum (pmTcDH H447Q), activated by crystal soaking with 1mM CuCl2 and 1 mM sodium ascorbate Authors: Varfolomeeva, L.A. / Shipkov, N.S. / Dergousova, N.I. / Boyko, K.M. / Tikhonova, T.V. / Popov, V.O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 221.6 KB | Display | ![]() |
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PDB format | ![]() | 170.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.1 MB | Display | ![]() |
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Full document | ![]() | 4.1 MB | Display | |
Data in XML | ![]() | 44.1 KB | Display | |
Data in CIF | ![]() | 68.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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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
#1: Protein | Mass: 54083.285 Da / Num. of mol.: 2 / Mutation: H447Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: FR698_09980 / Production host: ![]() ![]() #2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-CU / #4: Chemical | ChemComp-CL / | #5: 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: 2.21 Å3/Da / Density % sol: 44.35 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop Details: 0.1M HEPES, pH 7.5, 20% PEG 8000, 8% Ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 8, 2023 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.55→50 Å / Num. obs: 138679 / % possible obs: 99.5 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.125 / Rrim(I) all: 0.137 / Net I/σ(I): 13.32 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]()
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.582 Å2
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Refinement step | Cycle: 1 / Resolution: 1.55→45.85 Å
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Refine LS restraints |
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