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Yorodumi- PDB-4x8a: NavMS pore and C-terminal domain grown from protein purified in LiCl -
+Open data
-Basic information
Entry | Database: PDB / ID: 4x8a | |||||||||
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Title | NavMS pore and C-terminal domain grown from protein purified in LiCl | |||||||||
Components | Ion transport protein | |||||||||
Keywords | TRANSPORT PROTEIN / SELECTIVITY FILTER / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information voltage-gated sodium channel complex / membrane depolarization during action potential / voltage-gated sodium channel activity Similarity search - Function | |||||||||
Biological species | Magnetococcus sp. (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.02 Å | |||||||||
Authors | Naylor, C.E. / Bagneris, C. / Wallace, B.A. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Embo J. / Year: 2016 Title: Molecular basis of ion permeability in a voltage-gated sodium channel. Authors: Naylor, C.E. / Bagneris, C. / DeCaen, P.G. / Sula, A. / Scaglione, A. / Clapham, D.E. / Wallace, B.A. #1: Journal: Nat Commun / Year: 2013 Title: Role of the C-terminal domain in the structure and function of tetrameric sodium channels. Authors: Bagneris, C. / Decaen, P.G. / Hall, B.A. / Naylor, C.E. / Clapham, D.E. / Kay, C.W. / Wallace, B.A. #2: Journal: Nat Commun / Year: 2012 Title: Structure of a bacterial voltage-gated sodium channel pore reveals mechanisms of opening and closing. Authors: McCusker, E.C. / Bagneris, C. / Naylor, C.E. / Cole, A.R. / D'Avanzo, N. / Nichols, C.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 | 4x8a.cif.gz | 164.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4x8a.ent.gz | 130 KB | Display | PDB format |
PDBx/mmJSON format | 4x8a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4x8a_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 4x8a_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 4x8a_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 4x8a_validation.cif.gz | 20.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x8/4x8a ftp://data.pdbj.org/pub/pdb/validation_reports/x8/4x8a | HTTPS FTP |
-Related structure data
Related structure data | 4x88C 4x89C 5bzbC 4x87 C: citing same article (ref.) |
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Similar structure data |
-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: 16836.502 Da / Num. of mol.: 4 Fragment: NavMS pore and C-terminal domain, UNP residues 130-274 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Magnetococcus sp. (strain MC-1) (bacteria) Strain: MC-1 / Gene: Mmc1_0798 / Plasmid: PET15B / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: A0L5S6 #2: Chemical | ChemComp-2CV / #3: Chemical | #4: Chemical | ChemComp-NA / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 7.52 Å3/Da / Density % sol: 83.7 % / Description: Flat plates |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M NA3CITRATE, 0.1 M TRIS, PH 8.0, 34% PEG400 / PH range: 8 |
-Data collection
Diffraction | Mean temperature: 199 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.81568 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 7, 2013 |
Radiation | Monochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.81568 Å / Relative weight: 1 |
Reflection | Resolution: 3.02→45.56 Å / Num. all: 21664 / Num. obs: 21578 / % possible obs: 99.6 % / Redundancy: 8.3 % / Biso Wilson estimate: 64.16 Å2 / Rmerge(I) obs: 0.204 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 3.02→3.2 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.772 / Mean I/σ(I) obs: 3.4 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Resolution: 3.02→45.56 Å / Cor.coef. Fo:Fc: 0.8292 / Cor.coef. Fo:Fc free: 0.649 / SU R Cruickshank DPI: 0.371 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.361 / SU Rfree Blow DPI: 0.27 / SU Rfree Cruickshank DPI: 0.276
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Displacement parameters | Biso mean: 50.42 Å2
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Refine analyze | Luzzati coordinate error obs: 0.574 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.02→45.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.02→3.17 Å / Total num. of bins used: 11
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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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