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- PDB-6kq1: Crystal structure of cytochrome c551 from Pseudomonas sp. strain MT-1. -
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Open data
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Basic information
Entry | Database: PDB / ID: 6kq1 | |||||||||
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Title | Crystal structure of cytochrome c551 from Pseudomonas sp. strain MT-1. | |||||||||
![]() | Cytochrome C biogenesis protein CcsA | |||||||||
![]() | ELECTRON TRANSPORT / Cytochrome c551 / growth pressure / protein stability / Pseudomonas sp. strain MT-1. | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Fujii, S. / Oki, H. / Kawahara, K. / Ohkubo, T. / Masanari-Fujii, M. / Wakai, S. / Sambongi, Y. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into high stability of cytochrome c551 from a deep-sea piezo-tolerant bacterium, Pseudomonas sp. strain MT-1 Authors: Fujii, S. / Oki, H. / Kawahara, K. / Ohkubo, T. / Masanari-Fujii, M. / Wakai, S. / Sambongi, Y. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 54.3 KB | Display | ![]() |
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PDB format | ![]() | 37 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 12.2 KB | Display | |
Data in CIF | ![]() | 16.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 351cS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 8607.819 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | #4: 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: 2.39 Å3/Da / Density % sol: 48.61 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 10% (w/v) PEG 8000, 100 mM MES/ Sodium hydroxide pH 6.0, 200 mM Zinc acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 17, 2019 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.57→39.95 Å / Num. obs: 23763 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Net I/σ(I): 15 / Num. measured all: 309252 / Scaling rejects: 49 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 351C Resolution: 1.57→19.9783 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.97
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 72.99 Å2 / Biso mean: 24.8393 Å2 / Biso min: 10.87 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.57→19.9783 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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