+Open data
-Basic information
Entry | Database: PDB / ID: 5cbg | ||||||
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Title | Calcium activated non-selective cation channel | ||||||
Components | Ion transport 2 domain protein | ||||||
Keywords | TRANSPORT PROTEIN / membrane protein / calcium activated non-selective ion channel / 2TM helix ion channel family / tetrameric cation channel / ion transport | ||||||
Function / homology | Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / membrane / metal ion binding / Ion transport 2 domain protein Function and homology information | ||||||
Biological species | Tsukamurella paurometabola | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.14 Å | ||||||
Authors | Dhakshnamoorthy, B. / Rohaim, A. / Rui, H. / Blachowicz, L. / Roux, B. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2016 Title: Structural and functional characterization of a calcium-activated cation channel from Tsukamurella paurometabola. Authors: Dhakshnamoorthy, B. / Rohaim, A. / Rui, H. / Blachowicz, L. / Roux, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cbg.cif.gz | 131.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cbg.ent.gz | 103.8 KB | Display | PDB format |
PDBx/mmJSON format | 5cbg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5cbg_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5cbg_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5cbg_validation.xml.gz | 26 KB | Display | |
Data in CIF | 5cbg_validation.cif.gz | 34.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/5cbg ftp://data.pdbj.org/pub/pdb/validation_reports/cb/5cbg | HTTPS FTP |
-Related structure data
Related structure data | 5cbfC 5cbhC 2ahyS 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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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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Details | SEC-MALS indicates that the biological assembly is a tetramer. |
-Components
#1: Protein | Mass: 14118.424 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tsukamurella paurometabola (strain ATCC 8368 / DSM 20162 / JCM 10117 / NBRC 16120 / NCTC 13040) (bacteria) Strain: ATCC 8368 / DSM 20162 / JCM 10117 / NBRC 16120 / NCTC 13040 Gene: Tpau_1687 / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / References: UniProt: D5UM26 #2: Chemical | ChemComp-CA / #3: Sugar | #4: 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: 2.51 Å3/Da / Density % sol: 51.05 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG400, Cacodylate, Magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2012 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 3.14→50 Å / Num. obs: 14429 / % possible obs: 98.7 % / Redundancy: 4.9 % / Net I/σ(I): 3.35 |
Reflection shell | Resolution: 3.14→3.2 Å / Redundancy: 4.4 % / % possible all: 91.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2AHY Resolution: 3.14→47.9 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.844 / SU B: 19.04 / SU ML: 0.358 / Cross valid method: THROUGHOUT / ESU R Free: 0.563 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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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: 65.95 Å2
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Refinement step | Cycle: LAST / Resolution: 3.14→47.9 Å
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Refine LS restraints |
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