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- PDB-5aw6: Kinetics by X-ray crystallography: Rb+-substitution of bound K+ i... -
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Basic information
Entry | Database: PDB / ID: 5aw6 | |||||||||||||||
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Title | Kinetics by X-ray crystallography: Rb+-substitution of bound K+ in the E2.MgF42-.2K+ crystal after 5.5 min | |||||||||||||||
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![]() | HYDROLASE/TRANSPORT PROTEIN / MEMBRANE PROTEIN / ION PUMP / ATPASE / K+ BINDING / HALOACID DEHYDROGENEASE SUPERFAMILY / PHOSPHATE ANALOGUE / ATP-BINDING / HYDROLASE / ION TRANSPORT / NUCLEOTIDE-BINDING / PHOSPHOPROTEIN / HYDROLASE-TRANSPORT PROTEIN COMPLEX / KINETICS | |||||||||||||||
Function / homology | ![]() regulation of monoatomic ion transport / P-type sodium:potassium-exchanging transporter activity / sodium:potassium-exchanging ATPase complex / sodium ion export across plasma membrane / intracellular potassium ion homeostasis / intracellular sodium ion homeostasis / potassium ion import across plasma membrane / ATPase activator activity / sodium channel regulator activity / monoatomic ion transport ...regulation of monoatomic ion transport / P-type sodium:potassium-exchanging transporter activity / sodium:potassium-exchanging ATPase complex / sodium ion export across plasma membrane / intracellular potassium ion homeostasis / intracellular sodium ion homeostasis / potassium ion import across plasma membrane / ATPase activator activity / sodium channel regulator activity / monoatomic ion transport / proton transmembrane transport / sarcolemma / ATP hydrolysis activity / ATP binding / membrane / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Ogawa, H. / Cornelius, F. / Hirata, A. / Toyoshima, C. | |||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Sequential substitution of K(+) bound to Na(+),K(+)-ATPase visualized by X-ray crystallography. Authors: Ogawa, H. / Cornelius, F. / Hirata, A. / Toyoshima, 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 | ![]() | 269.7 KB | Display | ![]() |
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PDB format | ![]() | 209.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5avqC ![]() 5avrC ![]() 5avsC ![]() 5avtC ![]() 5avuC ![]() 5avvC ![]() 5avwC ![]() 5avxC ![]() 5avyC ![]() 5avzC ![]() 5aw0C ![]() 5aw1C ![]() 5aw2C ![]() 5aw3C ![]() 5aw4C ![]() 5aw5C ![]() 5aw7C ![]() 5aw8C ![]() 5aw9C ![]() 2zxeS 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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Unit cell |
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Components
-Protein , 3 types, 3 molecules ABG
#1: Protein | Mass: 113309.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Protein | Mass: 35176.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#3: Protein | Mass: 8225.446 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Sugars , 2 types, 2 molecules ![](data/chem/img/NAG.gif)
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#10: Sugar | ChemComp-NAG / |
-Non-polymers , 6 types, 10 molecules ![](data/chem/img/MF4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/RB.gif)
![](data/chem/img/CLR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/RB.gif)
![](data/chem/img/CLR.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-MF4 / | ||||||
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#6: Chemical | ChemComp-MG / | ||||||
#7: Chemical | #8: Chemical | #9: Chemical | ChemComp-CLR / | #11: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.25 % |
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Crystal grow | Temperature: 298 K / Method: microdialysis / pH: 7 Details: PEG 3000, MPD, potassium acetate, potassium chloride, magnesium chloride, potassium fluoride, MES/TRIS |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: May 16, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.813 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 42125 / % possible obs: 96.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 8.5 Å2 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 2.8→2.88 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2ZXE Resolution: 2.8→14.98 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 6067316.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3.5 / Details: BULK SOLVENT MODEL USED, Rigid body refinement
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 23.33 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 94.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→14.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.97 Å / Rfactor Rfree error: 0.063 / Total num. of bins used: 6
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Xplor file |
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