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- PDB-8ajz: Serial femtosecond crystallography structure of CO bound ba3- typ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ajz | |||||||||||||||||||||
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Title | Serial femtosecond crystallography structure of CO bound ba3- type cytochrome c oxidase at 2 milliseconds after irradiation by a 532 nm laser | |||||||||||||||||||||
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![]() | ELECTRON TRANSPORT / Membrane protein / bioenergetics / lipidic cubic phase crystallization / serial femtosecond crystallography / pump- probe method | |||||||||||||||||||||
Function / homology | ![]() cytochrome-c oxidase / oxidative phosphorylation / cytochrome-c oxidase activity / : / membrane => GO:0016020 / copper ion binding / heme binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||
![]() | Safari, C. / Ghosh, S. / Andersson, R. / Johannesson, J. / Donoso, A.V. / Bath, P. / Bosman, R. / Dahl, P. / Nango, E. / Tanaka, R. ...Safari, C. / Ghosh, S. / Andersson, R. / Johannesson, J. / Donoso, A.V. / Bath, P. / Bosman, R. / Dahl, P. / Nango, E. / Tanaka, R. / Zoric, D. / Svensson, E. / Nakane, T. / Iwata, S. / Neutze, R. / Branden, G. | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Time-resolved serial crystallography to track the dynamics of carbon monoxide in the active site of cytochrome c oxidase. Authors: Safari, C. / Ghosh, S. / Andersson, R. / Johannesson, J. / Bath, P. / Uwangue, O. / Dahl, P. / Zoric, D. / Sandelin, E. / Vallejos, A. / Nango, E. / Tanaka, R. / Bosman, R. / Borjesson, P. / ...Authors: Safari, C. / Ghosh, S. / Andersson, R. / Johannesson, J. / Bath, P. / Uwangue, O. / Dahl, P. / Zoric, D. / Sandelin, E. / Vallejos, A. / Nango, E. / Tanaka, R. / Bosman, R. / Borjesson, P. / Dunevall, E. / Hammarin, G. / Ortolani, G. / Panman, M. / Tanaka, T. / Yamashita, A. / Arima, T. / Sugahara, M. / Suzuki, M. / Masuda, T. / Takeda, H. / Yamagiwa, R. / Oda, K. / Fukuda, M. / Tosha, T. / Naitow, H. / Owada, S. / Tono, K. / Nureki, O. / Iwata, S. / Neutze, R. / Branden, G. | |||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 206 KB | Display | ![]() |
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PDB format | ![]() | 140.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.8 MB | Display | ![]() |
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Full document | ![]() | 4.8 MB | Display | |
Data in XML | ![]() | 35.4 KB | Display | |
Data in CIF | ![]() | 48.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8k65C ![]() 8k6yC ![]() 5ndcS S: Starting model for refinement C: citing same article ( |
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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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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
-Cytochrome c oxidase subunit ... , 2 types, 2 molecules AB
#1: Protein | Mass: 63540.141 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 18581.299 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 3769.602 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 7 types, 202 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/HAS.gif)
![](data/chem/img/OLC.gif)
![](data/chem/img/CMO.gif)
![](data/chem/img/CUA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/HAS.gif)
![](data/chem/img/OLC.gif)
![](data/chem/img/CMO.gif)
![](data/chem/img/CUA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-CU / | ||||||
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#5: Chemical | ChemComp-HEM / | ||||||
#6: Chemical | ChemComp-HAS / | ||||||
#7: Chemical | ChemComp-OLC / ( #8: Chemical | ChemComp-CMO / | #9: Chemical | ChemComp-CUA / | #10: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.39 Å3/Da / Density % sol: 63.71 % |
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Crystal grow | Temperature: 298 K / Method: lipidic cubic phase / pH: 5.3 Details: 100 mM 2-Morpholinoethanesulfonic acid, 34-38 % PEG 400 (v/v), 1.4 M NaCl, pH 5.3 |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MPCCD / Detector: CCD / Date: Feb 21, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.66 Å / Relative weight: 1 |
Reflection | Resolution: 2→43.4 Å / Num. obs: 75202 / % possible obs: 100 % / Redundancy: 94.5 % / Biso Wilson estimate: 40.03 Å2 / CC1/2: 0.91 / Net I/σ(I): 3.97 |
Reflection shell | Resolution: 2→2.071 Å / Mean I/σ(I) obs: 1.43 / Num. unique obs: 7465 / CC1/2: 0.55 |
Serial crystallography sample delivery | Method: injection |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5NDC Resolution: 2→38.7 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2→38.7 Å
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