[English] 日本語
Yorodumi- PDB-2dpk: The Crystal Structure of the Primary Ca2+ Sensor of the Na+/Ca2+ ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dpk | ||||||
---|---|---|---|---|---|---|---|
Title | The Crystal Structure of the Primary Ca2+ Sensor of the Na+/Ca2+ Exchanger | ||||||
Components | Sodium/calcium exchanger 1 | ||||||
Keywords | METAL TRANSPORT / Calcium sensory domain / beta-sandwich / cis-proline / beta-bulge | ||||||
Function / homology | Function and homology information Reduction of cytosolic Ca++ levels / Sodium/Calcium exchangers / calcium:monoatomic cation antiporter activity involved in regulation of postsynaptic cytosolic calcium ion concentration / Ion homeostasis / calcium:sodium antiporter activity / cell communication / intracellular sodium ion homeostasis / sodium ion import across plasma membrane / ankyrin binding / positive regulation of the force of heart contraction ...Reduction of cytosolic Ca++ levels / Sodium/Calcium exchangers / calcium:monoatomic cation antiporter activity involved in regulation of postsynaptic cytosolic calcium ion concentration / Ion homeostasis / calcium:sodium antiporter activity / cell communication / intracellular sodium ion homeostasis / sodium ion import across plasma membrane / ankyrin binding / positive regulation of the force of heart contraction / calcium ion import across plasma membrane / 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: 2.5 Å | ||||||
Authors | Abramson, J. / Sawaya, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: The crystal structure of the primary Ca2+ sensor of the na+/ca2+ exchanger reveals a novel Ca2+ binding motif. Authors: Nicoll, D.A. / Sawaya, M. / Kwon, S. / Cascio, D. / Philipson, K.D. / Abramson, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2dpk.cif.gz | 35.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2dpk.ent.gz | 26.8 KB | Display | PDB format |
PDBx/mmJSON format | 2dpk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dp/2dpk ftp://data.pdbj.org/pub/pdb/validation_reports/dp/2dpk | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 16692.250 Da / Num. of mol.: 1 / Fragment: Ca2+ binding domain 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Canis lupus familiaris (dog) / Species: Canis lupus / Strain: familiaris / Plasmid: pQE32 / Cell (production host): M15pRep4 / Production host: Escherichia coli (E. coli) / References: UniProt: P23685 | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-GAI / | #4: Chemical | ChemComp-EPE / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.16 % |
---|
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
---|---|
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→90 Å / Num. all: 5791 / Num. obs: 5386 / % possible obs: 93 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
-Processing
Software | Name: REFMAC / Version: 5.2.0005 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→57.26 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.918 / SU B: 18.957 / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.468 / ESU R Free: 0.31 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.205 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→57.26 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.501→2.565 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 7.7946 Å / Origin y: 7.0462 Å / Origin z: 30.5266 Å
|