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Yorodumi- PDB-2qvm: The second Ca2+-binding domain of the Na+-Ca2+ exchanger is essen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qvm | ||||||
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Title | The second Ca2+-binding domain of the Na+-Ca2+ exchanger is essential for regulation: crystal structures and mutational analysis | ||||||
Components | Sodium/calcium exchanger 1 | ||||||
Keywords | METAL BINDING PROTEIN / calcium regulation / CBD2 / NCX / calcium binding domain | ||||||
Function / homology | Function and homology information calcium:monoatomic cation antiporter activity involved in regulation of postsynaptic cytosolic calcium ion concentration / calcium:sodium antiporter activity / cell communication / sodium ion import across plasma membrane / intracellular sodium ion homeostasis / calcium ion import / ankyrin binding / calcium ion import across plasma membrane / positive regulation of the force of heart contraction / sodium ion transmembrane transport ...calcium:monoatomic cation antiporter activity involved in regulation of postsynaptic cytosolic calcium ion concentration / calcium:sodium antiporter activity / cell communication / sodium ion import across plasma membrane / intracellular sodium ion homeostasis / calcium ion import / ankyrin binding / calcium ion import across plasma membrane / positive regulation of the force of heart contraction / sodium ion transmembrane transport / positive regulation of bone mineralization / response to muscle stretch / calcium ion transmembrane transport / sarcolemma / postsynapse / calmodulin binding / axon / calcium ion binding / nucleoplasm / plasma membrane Similarity search - Function | ||||||
Biological species | Canis lupus familiaris (dog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.703 Å | ||||||
Authors | Chaptal, V. / Mercado Besserer, G. / Abramson, J. / Cascio, D. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007 Title: The second Ca2+-binding domain of the Na+ Ca2+ exchanger is essential for regulation: crystal structures and mutational analysis Authors: Mercado Besserer, G. / Ottolia, M. / Nicoll, D.A. / Chaptal, V. / Cascio, D. / Philipson, K.D. / Abramson, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qvm.cif.gz | 41.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qvm.ent.gz | 27 KB | Display | PDB format |
PDBx/mmJSON format | 2qvm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qv/2qvm ftp://data.pdbj.org/pub/pdb/validation_reports/qv/2qvm | HTTPS FTP |
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-Related structure data
Related structure data | 2qvkSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 21648.385 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Canis lupus familiaris (dog) / Species: Canis lupus / Strain: familiaris / Gene: SLC8A1 / Plasmid: pET47 / Production host: Escherichia coli (E. coli) / References: UniProt: P23685 | ||
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#2: Chemical | #3: 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: 1.97 Å3/Da / Density % sol: 36.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 21% (w/v) PEG-3350, 0.1 M HEPES (pH 6.3), CBD2 at 15 mg/ml, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 27, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.703→48.8 Å / Num. obs: 12622 / % possible obs: 99.8 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 25.4 |
Reflection shell | Resolution: 1.703→1.76 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 3 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2QVK Resolution: 1.703→48.8 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.138 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.66 Å2
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Refinement step | Cycle: LAST / Resolution: 1.703→48.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.703→1.747 Å / Total num. of bins used: 20
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