+Open data
-Basic information
Entry | Database: PDB / ID: 6by2 | ||||||||||||
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Title | Closed and deep-inactivated conformation of KcsA-T75A mutant | ||||||||||||
Components |
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Keywords | MEMBRANE PROTEIN / KcsA / C-type inactivation / ion channel / potassium channel | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Mus musculus (house mouse) Streptomyces coelicolor (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||||||||
Authors | Labro, A.J. / Cortes, D.M. / Tilegenova, C. / Cuello, L.G. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 Title: Inverted allosteric coupling between activation and inactivation gates in K+channels. Authors: Labro, A.J. / Cortes, D.M. / Tilegenova, C. / Cuello, L.G. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6by2.cif.gz | 116.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6by2.ent.gz | 91.7 KB | Display | PDB format |
PDBx/mmJSON format | 6by2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6by2_validation.pdf.gz | 698.4 KB | Display | wwPDB validaton report |
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Full document | 6by2_full_validation.pdf.gz | 706.6 KB | Display | |
Data in XML | 6by2_validation.xml.gz | 22.4 KB | Display | |
Data in CIF | 6by2_validation.cif.gz | 30.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/by/6by2 ftp://data.pdbj.org/pub/pdb/validation_reports/by/6by2 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules C
#3: Protein | Mass: 10948.710 Da / Num. of mol.: 1 / Mutation: T75A, C90L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: ATCC BAA-471 / A3(2) / M145 / Gene: kcsA, skc1, SCO7660, SC10F4.33 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A333 |
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-Antibody , 2 types, 2 molecules AB
#1: Antibody | Mass: 23411.242 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse) |
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#2: Antibody | Mass: 23435.738 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse) |
-Non-polymers , 4 types, 126 molecules
#4: Chemical | ChemComp-F09 / | ||
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#5: Chemical | ChemComp-DGA / | ||
#6: Chemical | #7: 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: 4.03 Å3/Da / Density % sol: 69.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: PEG400, 50 mM magnesium acetate, 50 mM sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 23, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.2 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.35→50 Å / Num. obs: 38148 / % possible obs: 99.12 % / Redundancy: 3.7 % / Biso Wilson estimate: 50.63 Å2 / Rmerge(I) obs: 0.153 / Χ2: 0.99 / Net I/σ(I): 7.67 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→30.825 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.49
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 123.44 Å2 / Biso mean: 59.882 Å2 / Biso min: 28.9 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.35→30.825 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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