+Open data
-Basic information
Entry | Database: PDB / ID: 4p2z | |||||||||
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Title | Structure of NavMS T207A/F214A | |||||||||
Components | Ion transport proteinIon transporter | |||||||||
Keywords | TRANSPORT PROTEIN / mutant / sodium channel / pore / membrane protein | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Magnetococcus sp. (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.08 Å | |||||||||
Authors | Bagneris, C. / Naylor, C.E. / Wallace, B.A. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: Prokaryotic NavMs channel as a structural and functional model for eukaryotic sodium channel antagonism. Authors: Bagneris, C. / DeCaen, P.G. / Naylor, C.E. / Pryde, D.C. / Nobeli, I. / 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 | 4p2z.cif.gz | 171.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4p2z.ent.gz | 134.5 KB | Display | PDB format |
PDBx/mmJSON format | 4p2z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p2/4p2z ftp://data.pdbj.org/pub/pdb/validation_reports/p2/4p2z | HTTPS FTP |
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-Related structure data
Related structure data | 4cbcC 4oxsC 4p30C 4p9oC 4p9pC 4pa3C 4pa4C 4pa6C 4pa7C 4pa9C 3zjzS 4bha 4cal 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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2 |
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Unit cell |
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Components on special symmetry positions |
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Details | Gel filtration was used to confirm the tetrameric state |
-Components
#1: Protein | Mass: 16730.379 Da / Num. of mol.: 4 / Mutation: T207A, F214A Source method: isolated from a genetically manipulated source Details: Pore and C-terminal domain only. The initial 4 residues are from a sequence. Double mutation to eliminate compound binding in the fenestration. Source: (gene. exp.) Magnetococcus sp. (bacteria) / Strain: MC-1 / Gene: Mmc1_0798 / Plasmid: PET15b / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: A0L5S6 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-2CV / #5: Water | ChemComp-HOH / | |
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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: 4 Å3/Da / Density % sol: 69.26 % / Description: Flat rectangular plates |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1M Tris-HCl, pH8, 34% v/v PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 30, 2014 |
Radiation | Monochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 3.08→45.7 Å / Num. obs: 18905 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 75.45 Å2 / Rmerge(I) obs: 0.278 / Net I/av σ(I): 1.9 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 3.08→3.3 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.928 / Mean I/σ(I) obs: 1.6 / % possible all: 71.1 |
-Processing
Software | Name: BUSTER / Version: 2.10.0 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ZJZ Resolution: 3.08→45.68 Å / Cor.coef. Fo:Fc: 0.8698 / Cor.coef. Fo:Fc free: 0.8648 / SU R Cruickshank DPI: 0.534 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.513 / SU Rfree Blow DPI: 0.344 / SU Rfree Cruickshank DPI: 0.351
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Displacement parameters | Biso mean: 64.52 Å2
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Refine analyze | Luzzati coordinate error obs: 0.761 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: last / Resolution: 3.08→45.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.08→3.25 Å / Total num. of bins used: 10
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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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