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Yorodumi- PDB-6vw9: C-terminal regulatory domain of the chloride transporter KCC-1 fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vw9 | ||||||
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Title | C-terminal regulatory domain of the chloride transporter KCC-1 from C. elegans, proteolyzed during crystallization | ||||||
Components | (K+/Cl-Cotransporter) x 2 | ||||||
Keywords | TRANSPORT PROTEIN / Cation-chloride-cotransporter / Slc transporter / cytosolic domain | ||||||
Function / homology | Function and homology information potassium:chloride symporter activity / chloride ion homeostasis / potassium ion homeostasis / cell volume homeostasis / potassium ion import across plasma membrane / chloride transmembrane transport / chemical synaptic transmission / membrane => GO:0016020 / synapse / plasma membrane Similarity search - Function | ||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.8 Å | ||||||
Authors | Zimanyi, C.M. / Cheung, J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Structure / Year: 2020 Title: Structure of the Regulatory Cytosolic Domain of a Eukaryotic Potassium-Chloride Cotransporter. Authors: Zimanyi, C.M. / Guo, M. / Mahmood, A. / Hendrickson, W.A. / Hirsh, D. / Cheung, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vw9.cif.gz | 155.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vw9.ent.gz | 109.5 KB | Display | PDB format |
PDBx/mmJSON format | 6vw9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vw/6vw9 ftp://data.pdbj.org/pub/pdb/validation_reports/vw/6vw9 | HTTPS FTP |
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-Related 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: 26443.824 Da / Num. of mol.: 1 / Fragment: C-terminal regulatory domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: kcc-1, CELE_R13A1.2, R13A1.2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: S6FCX2 | ||||||
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#2: Protein | Mass: 8106.339 Da / Num. of mol.: 1 / Fragment: C-terminal regulatory domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: kcc-1, CELE_R13A1.2, R13A1.2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: S6FCX2 | ||||||
#3: Chemical | ChemComp-P33 / | ||||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | Sequence details | The protein was internally proteolyzed during crystallization, as demonstrated by gel ...The protein was internally proteolyzed during crystallization, as demonstrated by gel electrophoresis. It is uncertain how much was cleaved. It is assumed that the residues missing from the electron density represent the residues that were removed proteolytically | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.49 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M TRIS pH 8.5, 5% w/v PEG 8000, 20% w/v PEG 300, 10% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 24, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.796→40.79 Å / Num. obs: 34639 / % possible obs: 97.87 % / Redundancy: 9.4 % / Biso Wilson estimate: 43.2 Å2 / CC1/2: 0.999 / CC star: 1 / Rsym value: 0.072 / Net I/σ(I): 13.83 |
Reflection shell | Resolution: 1.796→1.86 Å / Redundancy: 9.4 % / Mean I/σ(I) obs: 0.73 / Num. unique obs: 29973 / CC1/2: 0.454 / CC star: 0.79 / % possible all: 91.01 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1.8→40.79 Å / SU ML: 0.2208 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.5095 / Stereochemistry target values: GeoStd + Monomer Library
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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 mean: 66.62 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→40.79 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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