+Open data
-Basic information
Entry | Database: PDB / ID: 7mhx | ||||||
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Title | KcsA E71V closed gate with Ba2+ | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / ion channel | ||||||
Function / homology | Potassium channel domain / Ion channel / monoatomic ion transmembrane transport / identical protein binding / plasma membrane / : / DIACYL GLYCEROL / pH-gated potassium channel KcsA Function and homology information | ||||||
Biological species | Mus musculus (house mouse) Streptomyces lividans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Rohaim, A. / Li, J. / Weingarth, M. / Roux, B. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: A distinct mechanism of C-type inactivation in the Kv-like KcsA mutant E71V. Authors: Rohaim, A. / Vermeulen, B.J.A. / Li, J. / Kummerer, F. / Napoli, F. / Blachowicz, L. / Medeiros-Silva, J. / Roux, B. / Weingarth, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7mhx.cif.gz | 220.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mhx.ent.gz | 176.9 KB | Display | PDB format |
PDBx/mmJSON format | 7mhx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mh/7mhx ftp://data.pdbj.org/pub/pdb/validation_reports/mh/7mhx | HTTPS FTP |
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-Related structure data
Related structure data | 7mhrC 7mjtC 7mk6C 7mubC 1k4cS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 13181.600 Da / Num. of mol.: 1 / Mutation: P2A, E71V, L90C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces lividans (bacteria) / Gene: kcsA, skc1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A334 |
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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 , 3 types, 22 molecules
#4: Chemical | ChemComp-BA / |
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#5: Chemical | ChemComp-DGA / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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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: 3.94 Å3/Da / Density % sol: 68.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 50 mM sodium acetate pH 5.5, 50 mM magnesium acetate, 25% PEG 400 |
-Data collection
Diffraction | Mean temperature: 98 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 3, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→77.58 Å / Num. obs: 21076 / % possible obs: 99.8 % / Redundancy: 6 % / CC1/2: 0.92 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.85→3 Å / Num. unique obs: 3082 / CC1/2: 0.14 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1K4C Resolution: 2.85→50.01 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.926 / SU B: 41.121 / SU ML: 0.333 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.615 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 260.04 Å2 / Biso mean: 70 Å2 / Biso min: 28.72 Å2
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Refinement step | Cycle: final / Resolution: 2.85→50.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.924 Å / Rfactor Rfree error: 0
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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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