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- PDB-1kfy: QUINOL-FUMARATE REDUCTASE WITH QUINOL INHIBITOR 2-[1-(4-CHLORO-PH... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1kfy | ||||||
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Title | QUINOL-FUMARATE REDUCTASE WITH QUINOL INHIBITOR 2-[1-(4-CHLORO-PHENYL)-ETHYL]-4,6-DINITRO-PHENOL | ||||||
![]() | (FUMARATE REDUCTASE ...) x 4 | ||||||
![]() | OXIDOREDUCTASE / fumarate reductase / succinate dehydrogenase / quinone / quinol / respiration / membrane protein | ||||||
Function / homology | ![]() : / succinate dehydrogenase activity / fermentation / fumarate metabolic process / succinate dehydrogenase / anaerobic electron transport chain / succinate dehydrogenase (quinone) activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / iron-sulfur cluster binding ...: / succinate dehydrogenase activity / fermentation / fumarate metabolic process / succinate dehydrogenase / anaerobic electron transport chain / succinate dehydrogenase (quinone) activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / iron-sulfur cluster binding / bacterial-type flagellum assembly / tricarboxylic acid cycle / FAD binding / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / DNA damage response / membrane / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Iverson, T.M. / Luna-Chavez, C. / Croal, L.R. / Cecchini, G. / Rees, D.C. | ||||||
![]() | ![]() Title: Crystallographic studies of the Escherichia coli quinol-fumarate reductase with inhibitors bound to the quinol-binding site. Authors: Iverson, T.M. / Luna-Chavez, C. / Croal, L.R. / Cecchini, G. / Rees, D.C. #1: ![]() Title: Structure of the Escherichia coli Fumarate Reductase Respiratory Complex Authors: Iverson, T.M. / Luna-Chavez, C. / Cecchini, G. / Rees, D.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 395.7 KB | Display | ![]() |
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PDB format | ![]() | 320.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 816.2 KB | Display | ![]() |
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Full document | ![]() | 911.2 KB | Display | |
Data in XML | ![]() | 57.4 KB | Display | |
Data in CIF | ![]() | 81.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1kf6SC ![]() 1l0vC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 |
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Unit cell |
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Components
-FUMARATE REDUCTASE ... , 4 types, 8 molecules AMBNCODP
#1: Protein | Mass: 66057.555 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 27021.885 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Protein | Mass: 14898.773 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #4: Protein | Mass: 13118.870 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 7 types, 15 molecules ![](data/chem/img/OAA.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/F3S.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/BRS.gif)
![](data/chem/img/CE1.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/F3S.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/BRS.gif)
![](data/chem/img/CE1.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: 3.7 Å3/Da / Density % sol: 66.8 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: PEG 5K MME, MgOAc, EDTA, Na Citrate, DTT, DNP-19, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 98 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→50 Å / Num. all: 38919 / Num. obs: 38919 / % possible obs: 91.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.2 % / Rsym value: 0.104 / Net I/σ(I): 12 |
Reflection shell | Resolution: 3.6→3.66 Å / Mean I/σ(I) obs: 4.1 / Rsym value: 0.301 / % possible all: 90.8 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 124660 / Rmerge(I) obs: 0.104 |
Reflection shell | *PLUS % possible obs: 90.8 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 4.1 |
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Processing
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Refinement | Method to determine structure: ISOMORPHOUS REPLACEMENT Starting model: PDB ENTRY 1KF6 Resolution: 3.6→50 Å / σ(F): 0 / Details: REFMAC WAS ALSO USED IN REFINEMENT
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Refinement step | Cycle: LAST / Resolution: 3.6→50 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 3.6 Å / Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 2.1 % / Rfactor obs: 0.264 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_bond_d / Dev ideal: 0.0165 |