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Yorodumi- PDB-6z8c: Crystal Structure of the Voltage-Gated Sodium Channel NavMs (F208... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6z8c | ||||||
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Title | Crystal Structure of the Voltage-Gated Sodium Channel NavMs (F208L) in complex with N-desmethyltamoxifen (3.2 A resolution) | ||||||
Components | Ion transport proteinIon transporter | ||||||
Keywords | METAL TRANSPORT / Voltage Gated Sodium Channel / Membrane protein | ||||||
Function / homology | Voltage-gated cation channel calcium and sodium / Voltage-dependent channel domain superfamily / monoatomic cation channel activity / Ion transport domain / Ion transport protein / plasma membrane / Chem-QBN / Ion transport protein Function and homology information | ||||||
Biological species | Magnetococcus marinus MC-1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Sula, A. / Hollingworth, D. / Wallace, B.A. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Mol.Cell / Year: 2021 Title: A tamoxifen receptor within a voltage-gated sodium channel. Authors: Sula, A. / Hollingworth, D. / Ng, L.C.T. / Larmore, M. / DeCaen, P.G. / Wallace, B.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6z8c.cif.gz | 129.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6z8c.ent.gz | 99.9 KB | Display | PDB format |
PDBx/mmJSON format | 6z8c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z8/6z8c ftp://data.pdbj.org/pub/pdb/validation_reports/z8/6z8c | HTTPS FTP |
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-Related structure data
Related structure data | 6sx5C 6sx7C 6sxcC 6sxeC 6sxfC 6sxgC 5hvxS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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 A
#1: Protein | Mass: 31185.730 Da / Num. of mol.: 1 / Mutation: F208L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Magnetococcus marinus MC-1 (bacteria) / Gene: Mmc1_0798 / Production host: Escherichia coli (E. coli) / References: UniProt: A0L5S6 |
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-Non-polymers , 5 types, 48 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-12P / | #5: Chemical | #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: 5.05 Å3/Da / Density % sol: 75.64 % / Description: Bipyramids |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.08 M Sodium chloride; 0.1 M MES pH 6.5; 37 % v/v PEG 400; 4% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96864 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96864 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→48.51 Å / Num. obs: 10937 / % possible obs: 100 % / Redundancy: 14.2 % / CC1/2: 0.99 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 3.2→3.42 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1934 / CC1/2: 0.81 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5HVX Resolution: 3.2→48.51 Å / Cor.coef. Fo:Fc: 0.82 / Cor.coef. Fo:Fc free: 0.869 / SU R Cruickshank DPI: 0.926 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.007 / SU Rfree Blow DPI: 0.388 / SU Rfree Cruickshank DPI: 0.389
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Displacement parameters | Biso max: 170.47 Å2 / Biso mean: 85.86 Å2 / Biso min: 30 Å2
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Refine analyze | Luzzati coordinate error obs: 0.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.2→48.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.24 Å / Rfactor Rfree error: 0 / Total num. of bins used: 29
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Refinement TLS params. | Method: refined / Origin x: 17.2622 Å / Origin y: 6.0845 Å / Origin z: 32.1706 Å
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Refinement TLS group | Selection details: { A|* } |