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Yorodumi- PDB-5jdl: Structural mechanisms of extracellular ion exchange and induced b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jdl | ||||||||||||||||||
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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 1mM Sr2+ | ||||||||||||||||||
Components | Uncharacterized membrane protein MJ0091 | ||||||||||||||||||
Keywords | MEMBRANE PROTEIN / Na+/Ca2+ exchange / Calcium signalling / membrane transporter / induced conformational change | ||||||||||||||||||
Function / homology | Function and homology information calcium, potassium:sodium antiporter activity / calcium ion transmembrane transport / calcium channel activity / intracellular calcium ion homeostasis / plasma membrane Similarity search - Function | ||||||||||||||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.904 Å | ||||||||||||||||||
Authors | Liao, J. / Jiang, Y.X. / Faraldo-Gomez, J.D. | ||||||||||||||||||
Funding support | United States, China, 5items
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Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2016 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: Journal: Science / Year: 2012 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jdl.cif.gz | 77.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jdl.ent.gz | 54.6 KB | Display | PDB format |
PDBx/mmJSON format | 5jdl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jd/5jdl ftp://data.pdbj.org/pub/pdb/validation_reports/jd/5jdl | HTTPS FTP |
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-Related structure data
Related structure data | 5hwxC 5hwyC 5hxcC 5hxeC 5hxhC 5hxrC 5hxsC 5hyaC 5jdfC 5jdgC 5jdhC 5jdmC 5jdnC 5jdqC 3v5uS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 32160.326 Da / Num. of mol.: 1 / Mutation: L2V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea) Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440 Gene: MJ0091 / Production host: Escherichia coli (E. coli) / References: UniProt: Q57556 |
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-Non-polymers , 6 types, 13 molecules
#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-OLC / ( #5: Chemical | #6: Chemical | ChemComp-1PE / | #7: Water | ChemComp-HOH / | |
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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: 2.69 Å3/Da / Density % sol: 54.21 % |
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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: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9793 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 1, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.9→50 Å / Num. obs: 7648 / % possible obs: 94.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 70.14 Å2 / Rmerge(I) obs: 0.124 / Net I/av σ(I): 18.971 / Net I/σ(I): 6.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3V5U Resolution: 2.904→41.051 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.96
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 135.23 Å2 / Biso mean: 68.8306 Å2 / Biso min: 39.81 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.904→41.051 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: 5
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