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Yorodumi- PDB-4pa7: Structure of NavMS pore and C-terminal domain crystallised in pre... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pa7 | |||||||||
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Title | Structure of NavMS pore and C-terminal domain crystallised in presence of channel blocking compound | |||||||||
Components | Ion transport protein | |||||||||
Keywords | TRANSPORT PROTEIN / channel blocking compound / sodium channel / pore / 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 / MOLECULAR REPLACEMENT / Resolution: 3.02 Å | |||||||||
Authors | Naylor, C.E. / Bagneris, C. / 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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Remark 0 | : statistics at the very beginning when nothing is done yet |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pa7.cif.gz | 169.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pa7.ent.gz | 132.7 KB | Display | PDB format |
PDBx/mmJSON format | 4pa7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pa7_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 4pa7_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 4pa7_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 4pa7_validation.cif.gz | 20.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pa/4pa7 ftp://data.pdbj.org/pub/pdb/validation_reports/pa/4pa7 | HTTPS FTP |
-Related structure data
Related structure data | 4cbcC 4oxsC 4p2zC 4p30C 4p9oC 4p9pC 4pa3C 4pa4C 4pa6C 4pa9C 3zjzS C: citing same article (ref.) S: Starting model for refinement |
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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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-Components
#1: Protein | Mass: 16836.502 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: pore and C-terminal domain / 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 | ChemComp-2CV / #3: Chemical | #4: Chemical | ChemComp-NA / #5: Water | ChemComp-HOH / | Nonpolymer details | THE CHANNEL PROTEIN WAS CRYSTALLIZED IN THE PRESENCE OF THE CHANNEL-BLOCKING COMPOUND 4- ...THE CHANNEL PROTEIN WAS CRYSTALLIZ | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.89 Å3/Da / Density % sol: 68.41 % / Description: flat rectangular plates |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M sodium citrate, 0.1 M TRIS, pH 8.0, 34 % PEG |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.91966 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 21, 2003 |
Radiation | Monochromator: Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91966 Å / Relative weight: 1 |
Reflection | Resolution: 3.02→45.2 Å / Num. obs: 21117 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 64.32 Å2 / Rmerge(I) obs: 0.167 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 3.02→3.21 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 3.4 / % possible all: 99 |
-Processing
Software | Name: BUSTER / Version: 2.10.0 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: using 3ZJZ as a starting molecule Resolution: 3.02→45.2 Å / Cor.coef. Fo:Fc: 0.8828 / Cor.coef. Fo:Fc free: 0.9048 / SU R Cruickshank DPI: 0.437 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.427 / SU Rfree Blow DPI: 0.295 / SU Rfree Cruickshank DPI: 0.301
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Displacement parameters | Biso mean: 73.78 Å2
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Refine analyze | Luzzati coordinate error obs: 0.715 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.02→45.2 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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