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- PDB-5jdm: Structural mechanisms of extracellular ion exchange and induced b... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5jdm | ||||||||||||||||||
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Title | Structural mechanisms of extracellular ion exchange and induced binding-site occlusion in the sodium-calcium exchanger NCX_Mj soaked with 2.5 mM Na+ and 0.1mM Sr2+ | ||||||||||||||||||
![]() | sodium-calcium exchanger NCX_Mj | ||||||||||||||||||
![]() | MEMBRANE PROTEIN / Na+/Ca2+ exchange / Calcium signalling / membrane transporter / induced conformational change | ||||||||||||||||||
Function / homology | ![]() calcium, potassium:sodium antiporter activity / calcium ion transmembrane transport / calcium channel activity / intracellular calcium ion homeostasis / plasma membrane Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||
![]() | Liao, J. / Jiang, Y.X. / Faraldo-Gomez, J.D. | ||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Mechanism of extracellular ion exchange and binding-site occlusion in a sodium/calcium exchanger. Authors: Liao, J. / Marinelli, F. / Lee, C. / Huang, Y. / Faraldo-Gomez, J.D. / Jiang, Y. #1: ![]() Title: Structural insight into the ion-exchange mechanism of the sodium/calcium exchanger. Authors: Liao, J. / Li, H. / Zeng, W. / Sauer, D.B. / Belmares, R. / Jiang, Y. | ||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 78.2 KB | Display | ![]() |
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PDB format | ![]() | 54.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 931.1 KB | Display | ![]() |
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Full document | ![]() | 938.6 KB | Display | |
Data in XML | ![]() | 13.5 KB | Display | |
Data in CIF | ![]() | 17.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5hwxC ![]() 5hwyC ![]() 5hxcC ![]() 5hxeC ![]() 5hxhC ![]() 5hxrC ![]() 5hxsC ![]() 5hyaC ![]() 5jdfC ![]() 5jdgC ![]() 5jdhC ![]() 5jdlC ![]() 5jdnC ![]() 5jdqC ![]() 3v5uS 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 , 1 types, 1 molecules A
#1: Protein | Mass: 32217.379 Da / Num. of mol.: 1 / Mutation: L2V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440 Gene: MJ0091 / Production host: ![]() ![]() |
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-Non-polymers , 7 types, 22 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/SR.gif)
![](data/chem/img/OLC.gif)
![](data/chem/img/MYS.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/P3G.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SR.gif)
![](data/chem/img/OLC.gif)
![](data/chem/img/MYS.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/P3G.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-SR / | #4: Chemical | #5: Chemical | ChemComp-MYS / #6: Chemical | #7: Chemical | ChemComp-P3G / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.56 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / Details: PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 1, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.54→50 Å / Num. obs: 11536 / % possible obs: 99.9 % / Redundancy: 7.1 % / Biso Wilson estimate: 53.12 Å2 / Rmerge(I) obs: 0.119 / Net I/av σ(I): 21.471 / Net I/σ(I): 7.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3V5U Resolution: 2.558→37.64 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.03
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 175.83 Å2 / Biso mean: 62.1786 Å2 / Biso min: 32.02 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.558→37.64 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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