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- PDB-4yt0: Crystal structure of Mitochondrial rhodoquinol-fumarate reductase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4yt0 | ||||||
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Title | Crystal structure of Mitochondrial rhodoquinol-fumarate reductase from Ascaris suum with 2-methyl-N-[3-(1-methylethoxy)phenyl]benzamide. | ||||||
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![]() | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / rhodoquinol-fumarate reductase / Complex II / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
Function / homology | ![]() TIM22 mitochondrial import inner membrane insertion complex / : / mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase / succinate dehydrogenase (quinone) activity / protein insertion into mitochondrial inner membrane / oxidoreductase activity, acting on the CH-CH group of donors / 3 iron, 4 sulfur cluster binding / protein transmembrane transporter activity / ubiquinone binding ...TIM22 mitochondrial import inner membrane insertion complex / : / mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase / succinate dehydrogenase (quinone) activity / protein insertion into mitochondrial inner membrane / oxidoreductase activity, acting on the CH-CH group of donors / 3 iron, 4 sulfur cluster binding / protein transmembrane transporter activity / ubiquinone binding / tricarboxylic acid cycle / respiratory electron transport chain / mitochondrial membrane / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / mitochondrial inner membrane / electron transfer activity / heme binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Harada, S. / Shiba, T. / Sato, D. / Yamamoto, A. / Nagahama, M. / Yone, A. / Inaoka, D.K. / Sakamoto, K. / Inoue, M. / Honma, T. / Kita, K. | ||||||
![]() | ![]() Title: Structural Insights into the Molecular Design of Flutolanil Derivatives Targeted for Fumarate Respiration of Parasite Mitochondria Authors: Inaoka, D.K. / Shiba, T. / Sato, D. / Balogun, E.O. / Sasaki, T. / Nagahama, M. / Oda, M. / Matsuoka, S. / Ohmori, J. / Honma, T. / Inoue, M. / Kita, K. / Harada, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 467.6 KB | Display | ![]() |
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PDB format | ![]() | 372.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 81.4 KB | Display | |
Data in CIF | ![]() | 107.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3abvC ![]() 3ae7C ![]() 3ae9C ![]() 3aeaC ![]() 4ysxSC ![]() 4ysyC ![]() 4yszC ![]() 4ytmC ![]() 4ytpC ![]() 4yxdC ![]() 5c2tC 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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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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Components
-Protein , 2 types, 4 molecules AECG
#1: Protein | Mass: 71392.203 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Protein | Mass: 21168.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Succinate dehydrogenase [ubiquinone] ... , 2 types, 4 molecules BFDH
#2: Protein | Mass: 31673.951 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #4: Protein | Mass: 17014.932 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Non-polymers , 7 types, 14 molecules ![](data/chem/img/MLI.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/FES.gif)
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![](data/chem/img/F3S.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/MRN.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/F3S.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/MRN.gif)
#5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | #9: Chemical | #10: Chemical | #11: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.11 % |
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Crystal grow | Temperature: 293 K / Method: microdialysis / pH: 8.4 Details: 15% (W/V) PEG 3350, 100MM TRIS-HCL, 200MM NACL, 1MM SODIUM MALONATE, 0.06% (W/V) C12E8, 0.04% (W/V) C12M |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 2, 2014 |
Radiation | Monochromator: double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.65→50 Å / Num. obs: 37582 / % possible obs: 97.3 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.164 / Net I/σ(I): 4.5 |
Reflection shell | Resolution: 3.65→3.71 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 2.4 / % possible all: 94.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4YSX Resolution: 3.66→20 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.835 / SU B: 36.061 / SU ML: 0.513 / Cross valid method: THROUGHOUT / ESU R Free: 0.769 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 59.165 Å2
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Refinement step | Cycle: LAST / Resolution: 3.66→20 Å
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Refine LS restraints |
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