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Yorodumi- PDB-4ytm: Crystal structure of Mitochondrial rhodoquinol-fumarate reductase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ytm | ||||||
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Title | Crystal structure of Mitochondrial rhodoquinol-fumarate reductase from Ascaris suum with N-biphenyl-3-yl-2-(trifluoromethyl)benzamide | ||||||
Components |
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Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / OXIDOREDUCTASE / rhodoquinol-fumarate reductase / Complex II / Inhibitor / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
Function / homology | Function and homology information TIM22 mitochondrial import inner membrane insertion complex / mitochondrial respiratory chain complex II, succinate dehydrogenase complex (ubiquinone) / mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase / protein insertion into mitochondrial inner membrane / succinate dehydrogenase (quinone) activity / oxidoreductase activity, acting on the CH-CH group of donors / 3 iron, 4 sulfur cluster binding / ubiquinone binding / protein transmembrane transporter activity ...TIM22 mitochondrial import inner membrane insertion complex / mitochondrial respiratory chain complex II, succinate dehydrogenase complex (ubiquinone) / mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase / protein insertion into mitochondrial inner membrane / succinate dehydrogenase (quinone) activity / oxidoreductase activity, acting on the CH-CH group of donors / 3 iron, 4 sulfur cluster binding / ubiquinone binding / protein transmembrane transporter activity / 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 | Ascaris suum (pig roundworm) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||
Authors | Harada, S. / Shiba, T. / Sato, D. / Yamamoto, A. / Nagahama, M. / Yone, A. / Inaoka, D.K. / Sakamoto, K. / Inoue, M. / Honma, T. / Kita, K. | ||||||
Citation | Journal: Int J Mol Sci / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ytm.cif.gz | 473.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ytm.ent.gz | 375.6 KB | Display | PDB format |
PDBx/mmJSON format | 4ytm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yt/4ytm ftp://data.pdbj.org/pub/pdb/validation_reports/yt/4ytm | HTTPS FTP |
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-Related structure data
Related structure data | 3abvC 3ae7C 3ae9C 3aeaC 4ysxSC 4ysyC 4yszC 4yt0C 4ytpC 4yxdC 5c2tC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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) Ascaris suum (pig roundworm) / References: UniProt: U1LRQ3 #3: Protein | Mass: 21168.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ascaris suum (pig roundworm) / References: UniProt: P92506, UniProt: F1LC27*PLUS |
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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) Ascaris suum (pig roundworm) / References: UniProt: O44074, succinate dehydrogenase #4: Protein | Mass: 17014.932 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ascaris suum (pig roundworm) / References: UniProt: P92507 |
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-Non-polymers , 8 types, 15 molecules
#5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | #9: Chemical | #10: Chemical | #11: Chemical | #12: Chemical | ChemComp-EPH / | |
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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: 3.06 Å3/Da / Density % sol: 59.74 % |
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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: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: Bruker DIP-6040 / Detector: IMAGE PLATE / Date: Nov 28, 2007 |
Radiation | Monochromator: double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→50 Å / Num. obs: 49409 / % possible obs: 95.6 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 3.4→3.52 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.7 / % possible all: 93 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YSX Resolution: 3.4→20 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.886 / SU B: 23.895 / SU ML: 0.383 / Cross valid method: THROUGHOUT / ESU R Free: 0.559 / 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: 78.59 Å2
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Refinement step | Cycle: LAST / Resolution: 3.4→20 Å
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Refine LS restraints |
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