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Yorodumi- PDB-3eyw: Crystal structure of the C-terminal domain of E. coli KefC in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3eyw | ||||||
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Title | Crystal structure of the C-terminal domain of E. coli KefC in complex with KefF | ||||||
Components | C-terminal domain of Glutathione-regulated potassium-efflux system protein kefC fused to full length Glutathione-regulated potassium-efflux system ancillary protein kefF | ||||||
Keywords | TRANSPORT PROTEIN / KTN / RCK / K+ channel / K+ transport / KefC / K+ efflux / channel regulation / Antiport / Inner membrane / Ion transport / Membrane / Potassium / Potassium transport / Transmembrane | ||||||
Function / homology | Function and homology information glutathione-regulated potassium exporter activity / response to methylglyoxal / NADPH dehydrogenase (quinone) activity / potassium:proton antiporter complex / NAD(P)H dehydrogenase (quinone) / intracellular pH elevation / NADH:ubiquinone reductase (non-electrogenic) activity / regulation of pH / NAD(P)H dehydrogenase (quinone) activity / positive regulation of potassium ion transmembrane transport ...glutathione-regulated potassium exporter activity / response to methylglyoxal / NADPH dehydrogenase (quinone) activity / potassium:proton antiporter complex / NAD(P)H dehydrogenase (quinone) / intracellular pH elevation / NADH:ubiquinone reductase (non-electrogenic) activity / regulation of pH / NAD(P)H dehydrogenase (quinone) activity / positive regulation of potassium ion transmembrane transport / antiporter activity / toxic substance binding / proton transmembrane transport / regulation of intracellular pH / response to hydrogen peroxide / potassium ion transport / response to toxic substance / FMN binding / electron transfer activity / nucleotide binding / enzyme binding / protein homodimerization activity / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Roosild, T.P. | ||||||
Citation | Journal: Structure / Year: 2009 Title: KTN (RCK) Domains Regulate K(+) Channels and Transporters by Controlling the Dimer-Hinge Conformation. Authors: Roosild, T.P. / Castronovo, S. / Miller, S. / Li, C. / Rasmussen, T. / Bartlett, W. / Gunasekera, B. / Choe, S. / Booth, I.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3eyw.cif.gz | 160 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3eyw.ent.gz | 122.8 KB | Display | PDB format |
PDBx/mmJSON format | 3eyw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ey/3eyw ftp://data.pdbj.org/pub/pdb/validation_reports/ey/3eyw | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 5 / Auth seq-ID: 450 - 455 / Label seq-ID: 55 - 60
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Details | Biological unit is the same as the asymmetric unit |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 46557.844 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: KefC C-terminal domain fused to KefF / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: kefC, trkC and kefF, yabF / Plasmid: pHis8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03819, UniProt: P0A754 |
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-Non-polymers , 5 types, 188 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-MG / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | KEFC C-TERMINAL DOMAIN FUSED TO KEFF |
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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: 2.77 Å3/Da / Density % sol: 55.68 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 12% MPD, 10% PEG 3350, 60mM MgCl2, 100mM HEPES pH 7.0, 1mM NAD+, 1mM HALESDIE peptide, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 9, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 39348 / Num. obs: 39230 / % possible obs: 99.7 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 5.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 2QR2, 1LSS Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.909 / SU B: 6.412 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.292 / ESU R Free: 0.225 / 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: 29.374 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.4→2.46 Å / Total num. of bins used: 20
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