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- PDB-6n2o: 2-oxoglutarate:ferredoxin oxidoreductase from Magnetococcus marin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6n2o | |||||||||
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Title | 2-oxoglutarate:ferredoxin oxidoreductase from Magnetococcus marinus with 2-oxoglutarate, coenzyme A and succinyl-CoA bound | |||||||||
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![]() | OXIDOREDUCTASE / thiamine pyrophosphate / [4Fe-4S] cluster / carbon fixation / reductive tricarboxylic acid cycle / rTCA / 2-oxoglutarate:ferredoxin oxidoreductase / electron transfer | |||||||||
Function / homology | ![]() oxidoreductase activity, acting on the aldehyde or oxo group of donors / thiamine pyrophosphate binding / catalytic activity Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Chen, P.Y.-T. / Drennan, C.L. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: A reverse TCA cycle 2-oxoacid:ferredoxin oxidoreductase that makes C-C bonds from CO2. Authors: Chen, P.Y. / Li, B. / Drennan, C.L. / Elliott, 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 | ![]() | 341.4 KB | Display | ![]() |
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PDB format | ![]() | 268.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 59.1 KB | Display | |
Data in CIF | ![]() | 78.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6n2nSC 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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Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 62159.688 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC BAA-1437 / JCM 17883 / MC-1 / Gene: Mmc1_1749 / Production host: ![]() ![]() #2: Protein | Mass: 31706.275 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC BAA-1437 / JCM 17883 / MC-1 / Gene: Mmc1_1750 / Production host: ![]() ![]() |
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-Non-polymers , 7 types, 31 molecules ![](data/chem/img/AKG.gif)
![](data/chem/img/COA.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/TPP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SCA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/COA.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/TPP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SCA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-AKG / | ||||||||
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#4: Chemical | ChemComp-COA / | ||||||||
#5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-SCA / | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.38 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop Details: 27% (w/v) PEG 4000 and 0.08 M sodium cacodylate pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 13, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→100 Å / Num. obs: 38629 / % possible obs: 90.7 % / Redundancy: 8.1 % / Rsym value: 0.133 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.8→2.9 Å / Num. unique obs: 2935 / CC1/2: 0.857 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6N2N Resolution: 2.824→90.006 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.8
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.824→90.006 Å
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Refine LS restraints |
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LS refinement shell |
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