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- PDB-6zfu: Crystal structure of bovine cytochrome bc1 in complex with quinol... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6zfu | |||||||||
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Title | Crystal structure of bovine cytochrome bc1 in complex with quinolone inhibitor RKA066 | |||||||||
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![]() | ELECTRON TRANSPORT / cytochrome bc1 / malaria | |||||||||
Function / homology | ![]() Respiratory electron transport / mitochondrial respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / Mitochondrial protein degradation / respirasome / ubiquinone binding / respiratory electron transport chain / mitochondrial membrane ...Respiratory electron transport / mitochondrial respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / Mitochondrial protein degradation / respirasome / ubiquinone binding / respiratory electron transport chain / mitochondrial membrane / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / oxidoreductase activity / heme binding / mitochondrion / proteolysis / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Amporndanai, K. / O'Neill, P.M. / Hong, W.D. / Amewu, R.K. / Pidathala, C. / Berry, N.G. / Biagini, G.A. / Leung, S.C. / Hasnain, S.S. / Antonyuk, S.V. | |||||||||
![]() | ![]() Title: Targeting the ubiquinol-reduction (Qi) site of the mitochondrial cytochrome bc1 complex for the development of next generation quinolone antimalarials Authors: Amporndanai, K. / O'Neill, P.M. / Hong, W.D. / Amewu, R.K. / Pidathala, C. / Berry, N. / Biangini, G.A. / Leung, S.C. / Hasnain, S.S. / Antonyuk, S.V. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 848.3 KB | Display | ![]() |
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PDB format | ![]() | 692.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.3 MB | Display | ![]() |
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Full document | ![]() | 3.4 MB | Display | |
Data in XML | ![]() | 74.5 KB | Display | |
Data in CIF | ![]() | 98.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6zfsC ![]() 6zftC ![]() 5okdS 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
-Cytochrome b-c1 complex subunit ... , 8 types, 8 molecules ABEFGHIJ
#1: Protein | Mass: 49062.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Protein | Mass: 44730.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#5: Protein | Mass: 21640.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#6: Protein | Mass: 12356.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#7: Protein | Mass: 8799.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#8: Protein | Mass: 7628.592 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#9: Protein/peptide | Mass: 4827.567 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#10: Protein | Mass: 6866.897 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Protein , 2 types, 2 molecules CD
#3: Protein | Mass: 42489.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#4: Protein | Mass: 27107.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Sugars , 1 types, 1 molecules ![](data/chem/img/LMT.gif)
#15: Sugar | ChemComp-LMT / |
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-Non-polymers , 11 types, 27 molecules ![](data/chem/img/PG4.gif)
![](data/chem/img/6PE.gif)
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![](data/chem/img/HEM.gif)
![](data/chem/img/PEE.gif)
![](data/chem/img/JHE.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/FES.gif)
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![](data/chem/img/HOH.gif)
![](data/chem/img/6PE.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/PEE.gif)
![](data/chem/img/JHE.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/PX4.gif)
![](data/chem/img/HOH.gif)
#11: Chemical | #12: Chemical | ChemComp-6PE / | #13: Chemical | ChemComp-CDL / #14: Chemical | #16: Chemical | #17: Chemical | ChemComp-JHE / | #18: Chemical | ChemComp-HEC / | #19: Chemical | ChemComp-PO4 / #20: Chemical | ChemComp-FES / | #21: Chemical | ChemComp-PX4 / | #22: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.9 Å3/Da / Density % sol: 74.89 % / Description: Bipyramidal red crystal |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: Protein 40mg/mL with 1.6% HECAMEG; reservoir solution 50mM KPi pH 6.8, 100mM NaCl, 3mM NaN3, 10-13% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 4, 2017 / Details: mirrors | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 3.5→89.85 Å / Num. obs: 57461 / % possible obs: 100 % / Redundancy: 9 % / CC1/2: 0.987 / Rmerge(I) obs: 0.271 / Rpim(I) all: 0.093 / Rrim(I) all: 0.288 / Net I/σ(I): 5 / Num. measured all: 515936 / Scaling rejects: 9922 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5OKD Resolution: 3.5→89.85 Å / Cor.coef. Fo:Fc: 0.878 / Cor.coef. Fo:Fc free: 0.881 / SU B: 65.133 / SU ML: 0.409 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.464 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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 max: 306.89 Å2 / Biso mean: 140.473 Å2 / Biso min: 9.44 Å2
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Refinement step | Cycle: final / Resolution: 3.5→89.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.5→3.591 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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