+Open data
-Basic information
Entry | Database: PDB / ID: 7mjt | ||||||
---|---|---|---|---|---|---|---|
Title | KcsA open gate E71V mutant with Barium | ||||||
Components |
| ||||||
Keywords | MEMBRANE PROTEIN / ion channel | ||||||
Function / homology | Potassium channel domain / Ion channel / monoatomic ion transmembrane transport / identical protein binding / plasma membrane / : / pH-gated potassium channel KcsA Function and homology information | ||||||
Biological species | synthetic construct (others) Streptomyces lividans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Rohaim, A. / Li, J. / Weingarth, M. / Roux, B. | ||||||
Funding support | United States, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7mjt.cif.gz | 209.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7mjt.ent.gz | 167.9 KB | Display | PDB format |
PDBx/mmJSON format | 7mjt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mj/7mjt ftp://data.pdbj.org/pub/pdb/validation_reports/mj/7mjt | HTTPS FTP |
---|
-Related structure data
Related structure data | 7mhrC 7mhxC 7mk6C 7mubC 5vk6S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Antibody | Mass: 24379.131 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
---|---|
#2: Antibody | Mass: 23604.207 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
#3: Protein | Mass: 10133.879 Da / Num. of mol.: 1 / Mutation: A28C, E71V, L90C, R117Q, E118C, E120Q, R121Q 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 |
#4: Chemical | ChemComp-BA / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.92 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 50 mM sodium/ammonium acetate pH 5.5, 50 mM Magnesium acetate, 25% PG 400 |
-Data collection
Diffraction | Mean temperature: 98 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 28, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→99.34 Å / Num. obs: 10372 / % possible obs: 99.9 % / Redundancy: 6 % / CC1/2: 0.995 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 3.3→3.56 Å / Num. unique obs: 2117 / CC1/2: 0.649 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5vk6 Resolution: 3.3→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 81.069 / SU ML: 0.556 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.561 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 351.34 Å2 / Biso mean: 151.064 Å2 / Biso min: 90.26 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.3→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.3→3.383 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|