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Yorodumi- PDB-5hwx: Structural mechanisms of extracellular ion exchange and induced b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hwx | ||||||||||||||||||
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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 zero Ca2+ | ||||||||||||||||||
Components | sodium,calcium exchanger | ||||||||||||||||||
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: 2.4 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 | 5hwx.cif.gz | 73.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hwx.ent.gz | 52.2 KB | Display | PDB format |
PDBx/mmJSON format | 5hwx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hwx_validation.pdf.gz | 455.1 KB | Display | wwPDB validaton report |
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Full document | 5hwx_full_validation.pdf.gz | 456.8 KB | Display | |
Data in XML | 5hwx_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 5hwx_validation.cif.gz | 16.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hw/5hwx ftp://data.pdbj.org/pub/pdb/validation_reports/hw/5hwx | HTTPS FTP |
-Related structure data
Related structure data | 5hwyC 5hxcC 5hxeC 5hxhC 5hxrC 5hxsC 5hyaC 5jdfC 5jdgC 5jdhC 5jdlC 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 / Fragment: UNP residues 1-301 / 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, 28 molecules
#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-PEG / | #5: Chemical | ChemComp-1PE / | #6: Chemical | ChemComp-MYS / #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: 2.67 Å3/Da / Density % sol: 54.01 % |
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Crystal grow | Temperature: 298 K / Method: lipidic cubic phase / Details: PEG400 |
-Data collection
Diffraction | Mean temperature: 80 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 1, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→50 Å / Num. obs: 14024 / % possible obs: 99.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 47.19 Å2 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.04 / Rrim(I) all: 0.098 / Χ2: 1.349 / Net I/av σ(I): 24.176 / Net I/σ(I): 8.2 / Num. measured all: 97377 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3V5U Resolution: 2.4→39.923 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.33 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 105.39 Å2 / Biso mean: 53.5243 Å2 / Biso min: 34.77 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→39.923 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: 10
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