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Yorodumi- PDB-5hwy: Structural mechanisms of extracellular ion exchange and induced b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hwy | ||||||
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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 10 mM Na+ and zero Ca2+ | ||||||
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: 2.098 Å | ||||||
Authors | Liao, J. / Jiang, Y.X. / Faraldo-Gomez, J.D. | ||||||
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 | 5hwy.cif.gz | 78.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hwy.ent.gz | 56 KB | Display | PDB format |
PDBx/mmJSON format | 5hwy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hwy_validation.pdf.gz | 669.3 KB | Display | wwPDB validaton report |
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Full document | 5hwy_full_validation.pdf.gz | 671.4 KB | Display | |
Data in XML | 5hwy_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 5hwy_validation.cif.gz | 18.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hw/5hwy ftp://data.pdbj.org/pub/pdb/validation_reports/hw/5hwy | HTTPS FTP |
-Related structure data
Related structure data | 5hwxC 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: 32029.131 Da / Num. of mol.: 1 / Fragment: UNP residues 1-300 / 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, 56 molecules
#2: Chemical | ChemComp-OLC / ( | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-MYS / #5: Chemical | ChemComp-ACT / | #6: Chemical | ChemComp-1PE / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.45 % |
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Crystal grow | Temperature: 298 K / Method: lipidic cubic phase / Details: PEG 400 |
-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, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.098→50 Å / Num. obs: 19305 / % possible obs: 99.9 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.04 / Rrim(I) all: 0.101 / Χ2: 1.393 / Net I/av σ(I): 24.256 / Net I/σ(I): 10.1 / Num. measured all: 117734 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.098→36.022 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.97 / 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: 93.89 Å2 / Biso mean: 35.7621 Å2 / Biso min: 19.83 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.098→36.022 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: 11
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