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- PDB-8yts: The structure of the cytochrome c546/556 from Thioalkalivibrio pa... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8yts | ||||||
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Title | The structure of the cytochrome c546/556 from Thioalkalivibrio paradoxus with unusual UV-Vis spectral features at atomic resolution | ||||||
![]() | Cytochrome C | ||||||
![]() | ELECTRON TRANSPORT / Cytochrome c546/556 / Monoheme cytochrome / Q-bands splitting / room temperature / two conformations of the propianate group | ||||||
Function / homology | Cytochrome c / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / electron transfer activity / heme binding / metal ion binding / HEME C / Cytochrome C![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Varfolomeeva, L.A. / Solovieva, A.Y. / Dergousova, N.I. / Boyko, K.M. / Tikhonova, T.V. / Popov, V.O. | ||||||
Funding support | 1items
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![]() | ![]() Title: The structure of the cytochrome c546/556 from Thioalkalivibrio paradoxus with unusual UV-Vis spectral features at atomic resolution Authors: Varfolomeeva, L.A. / Solovieva, A.Y. / 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 | ![]() | 116.1 KB | Display | ![]() |
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PDB format | ![]() | 91.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 11.4 KB | Display | |
Data in CIF | ![]() | 16.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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: 11026.460 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: W0DLP1 #2: Chemical | #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 grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 3.5 / Details: 0.1 M Citric acid, pH 3.5, 30% PEG 3350 |
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-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: Jul 20, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→48.56 Å / Num. obs: 47379 / % possible obs: 98.5 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.022 / Rrim(I) all: 0.043 / Χ2: 0.56 / Net I/σ(I): 13.1 / Num. measured all: 165902 |
Reflection shell | Resolution: 1.15→1.17 Å / % possible obs: 95.7 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.174 / Num. measured all: 7250 / Num. unique obs: 2270 / CC1/2: 0.922 / Rpim(I) all: 0.108 / Rrim(I) all: 0.206 / Χ2: 0.13 / Net I/σ(I) obs: 1.9 |
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.26 Å2
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Refinement step | Cycle: 1 / Resolution: 1.15→48.56 Å
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Refine LS restraints |
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