+Open data
-Basic information
Entry | Database: PDB / ID: 8ayp | |||||||||||||||
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Title | NaK C-DI mutant with Rb+ and Ba2+ | |||||||||||||||
Components | Potassium channel protein | |||||||||||||||
Keywords | TRANSPORT PROTEIN / ION CHANNEL / PROKARYOTE / MEMBRANE PROTEIN | |||||||||||||||
Function / homology | Function and homology information stabilization of membrane potential / potassium ion leak channel activity / outward rectifier potassium channel activity / identical protein binding / membrane / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | Bacillus cereus ATCC 14579 (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||||||||
Authors | Minniberger, S. / Plested, A.J.R. | |||||||||||||||
Funding support | European Union, Germany, 4items
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Citation | Journal: J.Chem.Inf.Model. / Year: 2023 Title: Mechanism of Calcium Permeation in a Glutamate Receptor Ion Channel. Authors: Schackert, F.K. / Biedermann, J. / Abdolvand, S. / Minniberger, S. / Song, C. / Plested, A.J.R. / Carloni, P. / Sun, H. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ayp.cif.gz | 194.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ayp.ent.gz | 131.9 KB | Display | PDB format |
PDBx/mmJSON format | 8ayp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ayp_validation.pdf.gz | 3.3 MB | Display | wwPDB validaton report |
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Full document | 8ayp_full_validation.pdf.gz | 3.2 MB | Display | |
Data in XML | 8ayp_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 8ayp_validation.cif.gz | 23.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/8ayp ftp://data.pdbj.org/pub/pdb/validation_reports/ay/8ayp | HTTPS FTP |
-Related structure data
Related structure data | 8ayqC 3e86S S: Starting model for refinement 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 10735.706 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus ATCC 14579 (bacteria) Strain: ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711 Gene: BC_0669 / Plasmid: pQE60 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q81HW2 #2: Chemical | ChemComp-MPD / ( #3: Chemical | ChemComp-RB / #4: Chemical | ChemComp-BA / #5: Water | ChemComp-HOH / | 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: 2.38 Å3/Da / Density % sol: 48.4 % / Description: thin plates |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 100 mM MES (NaOH), 40% v/v MPD (2-Methyl-2,4-pentanediol racemate) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 15, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 2.098→44.68 Å / Num. obs: 24497 / % possible obs: 99.37 % / Redundancy: 4.4 % / Biso Wilson estimate: 42.57 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.1153 / Rpim(I) all: 0.06133 / Rrim(I) all: 0.1311 / Net I/σ(I): 9.03 |
Reflection shell | Resolution: 2.098→2.173 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2383 / CC1/2: 0.393 / CC star: 0.751 / Rpim(I) all: 0.7703 / % possible all: 98.39 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Starting model: 3.0E+86 / Resolution: 2.1→44.68 Å / SU ML: 0.3047 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.8441 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 60.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→44.68 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 | Refine-ID: X-RAY DIFFRACTION
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