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Yorodumi- PDB-4yxd: CRYSTAL STRUCTURE OF PORCINE HEART MITOCHONDRIAL COMPLEX II BOUND... -
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-Basic information
Entry | Database: PDB / ID: 4yxd | ||||||
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Title | CRYSTAL STRUCTURE OF PORCINE HEART MITOCHONDRIAL COMPLEX II BOUND WITH flutolanil | ||||||
Components |
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Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / OXIDOREDUCTASE / SUCCINATE DEHYDROGENASE / Complex II / Inhibitor / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
Function / homology | Function and homology information Maturation of TCA enzymes and regulation of TCA cycle / Citric acid cycle (TCA cycle) / Oxidoreductases; Acting on the CH-OH group of donors; With a quinone or similar compound as acceptor / : / mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase / succinate dehydrogenase (quinone) activity / 3 iron, 4 sulfur cluster binding / ubiquinone binding / tricarboxylic acid cycle ...Maturation of TCA enzymes and regulation of TCA cycle / Citric acid cycle (TCA cycle) / Oxidoreductases; Acting on the CH-OH group of donors; With a quinone or similar compound as acceptor / : / mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase / succinate dehydrogenase (quinone) activity / 3 iron, 4 sulfur cluster binding / ubiquinone binding / tricarboxylic acid cycle / respiratory electron transport chain / mitochondrial membrane / aerobic respiration / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / mitochondrial inner membrane / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 | 4yxd.cif.gz | 239.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yxd.ent.gz | 182.3 KB | Display | PDB format |
PDBx/mmJSON format | 4yxd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4yxd_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 4yxd_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 4yxd_validation.xml.gz | 41.2 KB | Display | |
Data in CIF | 4yxd_validation.cif.gz | 55.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yx/4yxd ftp://data.pdbj.org/pub/pdb/validation_reports/yx/4yxd | HTTPS FTP |
-Related structure data
Related structure data | 3abvC 3ae7C 3ae9C 3aeaC 4ysxC 4ysyC 4yszC 4yt0C 4ytmC 4ytpC 5c2tC 1zoyS 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
-Succinate dehydrogenase [ubiquinone] ... , 3 types, 3 molecules ABD
#1: Protein | Mass: 72926.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q0QF01, succinate dehydrogenase |
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#2: Protein | Mass: 31627.658 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q007T0, succinate dehydrogenase |
#4: Protein | Mass: 17025.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A5GZW8 |
-Protein , 1 types, 1 molecules C
#3: Protein | Mass: 18540.057 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: D0VWV4 |
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-Non-polymers , 6 types, 6 molecules
#5: Chemical | ChemComp-FAD / |
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#6: Chemical | ChemComp-FES / |
#7: Chemical | ChemComp-SF4 / |
#8: Chemical | ChemComp-F3S / |
#9: Chemical | ChemComp-HEM / |
#10: Chemical | ChemComp-FTN / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 25MM HEPES-NAOH, 7% PEG 4000, 200MM SUCROSE, 100MM NACL, 10MM CACL2, 0.5MM EDTA, 3% 1,6-HAXANEDIOL,0.5% N-DECYL-BETA-D-MALTOSIDE |
-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: RAYONIX MX300HE / Detector: CCD / Date: Nov 1, 2013 |
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→50 Å / Num. obs: 35891 / % possible obs: 97.5 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.099 / Net I/av σ(I): 2.8 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 3→3.05 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.464 / % possible all: 95.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ZOY Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.915 / SU B: 18.46 / SU ML: 0.319 / Cross valid method: THROUGHOUT / ESU R Free: 0.406 / 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: 84.263 Å2
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Refinement step | Cycle: 1 / Resolution: 3→20 Å
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