+Open data
-Basic information
Entry | Database: PDB / ID: 3e9u | ||||||
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Title | Crystal structure of Calx CBD2 domain | ||||||
Components | Na/Ca exchange protein | ||||||
Keywords | MEMBRANE PROTEIN / CBD2 / Calx / Membrane / Transmembrane | ||||||
Function / homology | Function and homology information rhabdomere membrane / calcium:sodium antiporter activity / neuromuscular process controlling posture / phototransduction / calcium ion import across plasma membrane / sodium ion transmembrane transport / response to endoplasmic reticulum stress / sarcolemma / postsynapse / calmodulin binding ...rhabdomere membrane / calcium:sodium antiporter activity / neuromuscular process controlling posture / phototransduction / calcium ion import across plasma membrane / sodium ion transmembrane transport / response to endoplasmic reticulum stress / sarcolemma / postsynapse / calmodulin binding / axon / calcium ion binding Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Wu, M. / Zheng, L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Crystal structure of CBD2 from the Drosophila Na(+)/Ca(2+) exchanger: diversity of Ca(2+) regulation and its alternative splicing modification. Authors: Wu, M. / Wang, M. / Nix, J. / Hryshko, L.V. / Zheng, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3e9u.cif.gz | 44.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3e9u.ent.gz | 31.8 KB | Display | PDB format |
PDBx/mmJSON format | 3e9u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e9/3e9u ftp://data.pdbj.org/pub/pdb/validation_reports/e9/3e9u | HTTPS FTP |
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-Related structure data
Related structure data | |
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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
#1: Protein | Mass: 18360.662 Da / Num. of mol.: 1 / Fragment: Calx CBD2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Calx, NCX, CG5685 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl-21 / References: UniProt: Q24413 |
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#2: 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: 4.2 Å3/Da / Density % sol: 70.75 % |
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Crystal grow | Method: evaporation / pH: 8 Details: 0.2 M potassium formate, 10 mM CaCl2, 20% Polyethylene glycol 3350, pH 8.0, EVAPORATION |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å |
Detector | Type: NOIR-1 / Detector: CCD / Date: Apr 8, 2008 |
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→38.32 Å / Num. obs: 10260 / % possible obs: 99.8 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 2.5→2.55 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2.5 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→38.2 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.911 / SU B: 21.949 / SU ML: 0.232 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.335 / ESU R Free: 0.251 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.735 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→38.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 26.5525 Å / Origin y: -38.0112 Å / Origin z: -1.2815 Å
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Refinement TLS group |
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