[English] 日本語

- PDB-5avz: Kinetics by X-ray crystallography: Tl+-substitution of bound K+ i... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5avz | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Kinetics by X-ray crystallography: Tl+-substitution of bound K+ in the E2.MgF42-.2K+ crystal after 55 min | |||||||||||||||
![]() |
| |||||||||||||||
![]() | 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 / ATP hydrolysis activity / ATP binding / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Ogawa, H. / Cornelius, F. / Hirata, A. / Toyoshima, C. | |||||||||||||||
Funding support | ![]() ![]()
| |||||||||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 270.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 209.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 948.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 973.6 KB | Display | |
Data in XML | ![]() | 46.2 KB | Display | |
Data in CIF | ![]() | 62.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5avqC ![]() 5avrC ![]() 5avsC ![]() 5avtC ![]() 5avuC ![]() 5avvC ![]() 5avwC ![]() 5avxC ![]() 5avyC ![]() 5aw0C ![]() 5aw1C ![]() 5aw2C ![]() 5aw3C ![]() 5aw4C ![]() 5aw5C ![]() 5aw6C ![]() 5aw7C ![]() 5aw8C ![]() 5aw9C ![]() 2zxeS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
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) ![]() |
---|---|
#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 
#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 |
---|---|
#10: Sugar | ChemComp-NAG / |
-Non-polymers , 6 types, 8 molecules 










#5: Chemical | ChemComp-MF4 / | ||||||
---|---|---|---|---|---|---|---|
#6: Chemical | ChemComp-MG / | ||||||
#7: Chemical | #8: Chemical | ChemComp-K / | #9: Chemical | ChemComp-CLR / | #11: Water | ChemComp-HOH / | |
-Details
Has protein modification | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.35 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Dec 10, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. obs: 30155 / % possible obs: 99.7 % / Redundancy: 4.9 % / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 3.2→3.3 Å |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2ZXE Resolution: 3.2→14.99 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 2958455.91 / 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 59.58 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 128.2 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→14.99 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.2→3.4 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|