+Open data
-Basic information
Entry | Database: PDB / ID: 8thn | ||||||
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Title | KcsA M96V mutant with Y78ester in High K+ | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / Ion transport / Potassium ion channel / ester | ||||||
Function / homology | Potassium channel domain / Ion channel / monoatomic ion transmembrane transport / identical protein binding / plasma membrane / : / TETRABUTYLAMMONIUM ION / 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: 2.9 Å | ||||||
Authors | Reddi, R. / Valiyaveetil, F.I. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2023 Title: A facile approach for incorporating tyrosine esters to probe ion-binding sites and backbone hydrogen bonds. Authors: Reddi, R. / Chatterjee, S. / Matulef, K. / Gustafson, A. / Gao, L. / Valiyaveetil, F.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8thn.cif.gz | 115.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8thn.ent.gz | 87.3 KB | Display | PDB format |
PDBx/mmJSON format | 8thn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/th/8thn ftp://data.pdbj.org/pub/pdb/validation_reports/th/8thn | HTTPS FTP |
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-Related structure data
Related structure data | 8dhrC C: citing same article (ref.) |
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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: 10957.671 Da / Num. of mol.: 1 / Mutation: M96V, Y78ester 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: Homo sapiens (human) |
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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: Homo sapiens (human) |
-Non-polymers , 3 types, 6 molecules
#4: Chemical | ChemComp-K / #5: Chemical | ChemComp-TBA / | #6: Water | ChemComp-HOH / | |
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-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: 3.96 Å3/Da / Density % sol: 68.97 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.25 Details: 27% PEG 400 (v/v), 50 mM magnesium acetate, 50 mM MES pH 6.25 PH range: 6.0- 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 20, 2018 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→55.01 Å / Num. obs: 20234 / % possible obs: 99.9 % / Redundancy: 6.3 % / CC1/2: 0.98 / Net I/σ(I): 5.1 |
Reflection shell | Resolution: 2.9→3.08 Å / Num. unique obs: 3264 / CC1/2: 0.365 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→55.01 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.73 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→55.01 Å
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Refine LS restraints |
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LS refinement shell |
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