+Open data
-Basic information
Entry | Database: PDB / ID: 4f4l | ||||||
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Title | Open Channel Conformation of a Voltage Gated Sodium Channel | ||||||
Components | Ion transport proteinIon transporter | ||||||
Keywords | METAL TRANSPORT / alpha helical membrane protein / voltage-gated sodium channel / membrane | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Magnetococcus marinus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.49 Å | ||||||
Authors | McCusker, E.C. / Bagneris, C. / Naylor, C.E. / Cole, A.R. / D'Avanzo, N. / Nichols, C.G. / Wallace, B.A. | ||||||
Citation | 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 | 4f4l.cif.gz | 80.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4f4l.ent.gz | 60.9 KB | Display | PDB format |
PDBx/mmJSON format | 4f4l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f4/4f4l ftp://data.pdbj.org/pub/pdb/validation_reports/f4/4f4l | HTTPS FTP |
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-Related structure data
Related structure data | 3rvyS 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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Unit cell |
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-Components
#1: Protein | Mass: 12439.515 Da / Num. of mol.: 4 / Fragment: pore region (S5-C-terminal domain) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Magnetococcus marinus (bacteria) / Strain: MC-1 / Gene: A0L5S6, Mmc1_0798 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: A0L5S6 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 4.14 Å3/Da / Density % sol: 70.31 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 5.6 Details: 30% PEG 400, 0.09 M tri-sodium citrate, pH 5.6, VAPOR DIFFUSION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å | ||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 23, 2011 / Details: Si crystal | ||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.49→95.1 Å / Num. all: 10528 / Num. obs: 8747 / % possible obs: 83.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Biso Wilson estimate: 92.44 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.05 / Net I/σ(I): 22.98 | ||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3RVY Resolution: 3.49→43.62 Å / Cor.coef. Fo:Fc: 0.8956 / Cor.coef. Fo:Fc free: 0.8951 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 137.98 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.49→43.62 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5
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