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Yorodumi- PDB-6n2n: Crystal structure of 2-oxoglutarate:ferredoxin oxidoreductase fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6n2n | |||||||||
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Title | Crystal structure of 2-oxoglutarate:ferredoxin oxidoreductase from Magnetococcus marinus | |||||||||
Components |
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Keywords | OXIDOREDUCTASE / thiamine pyrophosphate / [4Fe-4S] cluster / carbon fixation / reductive tricarboxylic acid cycle / rTCA / 2-oxoglutarate:ferredoxin oxidoreductase / electron transfer | |||||||||
Function / homology | Function and homology information oxidoreductase activity, acting on the aldehyde or oxo group of donors / thiamine pyrophosphate binding / catalytic activity Similarity search - Function | |||||||||
Biological species | Magnetococcus marinus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.937 Å | |||||||||
Authors | Chen, P.Y.-T. / Drennan, C.L. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Joule / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6n2n.cif.gz | 376.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6n2n.ent.gz | 297.2 KB | Display | PDB format |
PDBx/mmJSON format | 6n2n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6n2n_validation.pdf.gz | 990.6 KB | Display | wwPDB validaton report |
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Full document | 6n2n_full_validation.pdf.gz | 1000.8 KB | Display | |
Data in XML | 6n2n_validation.xml.gz | 73.7 KB | Display | |
Data in CIF | 6n2n_validation.cif.gz | 110.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n2/6n2n ftp://data.pdbj.org/pub/pdb/validation_reports/n2/6n2n | HTTPS FTP |
-Related structure data
Related structure data | 6n2oC 3g2eS 4wbxS 5c4iS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Magnetococcus marinus (strain ATCC BAA-1437 / JCM 17883 / MC-1) (bacteria) Strain: ATCC BAA-1437 / JCM 17883 / MC-1 / Gene: Mmc1_1749 / Production host: Escherichia coli (E. coli) / References: UniProt: A0L8G4 #2: Protein | Mass: 31706.275 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Magnetococcus marinus (strain ATCC BAA-1437 / JCM 17883 / MC-1) (bacteria) Strain: ATCC BAA-1437 / JCM 17883 / MC-1 / Gene: Mmc1_1750 / Production host: Escherichia coli (E. coli) / References: UniProt: A0L8G5 |
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-Non-polymers , 5 types, 1517 molecules
#3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.51 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop Details: 14% (w/v) PEG 8000, 0.21-0.28 M (NH4)2SO4, and 0.10 M MES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 23, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.937→100 Å / Num. obs: 125663 / % possible obs: 97.6 % / Redundancy: 4 % / Rsym value: 0.106 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 1.937→2.01 Å / Num. unique obs: 11651 / CC1/2: 0.735 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WBX, 5C4I, 3G2E Resolution: 1.937→98.152 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.71
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.937→98.152 Å
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Refine LS restraints |
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LS refinement shell |
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