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Yorodumi- PDB-4cbc: Open-form NavMS Sodium Channel Pore (with C-terminal Domain) afte... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cbc | ||||||
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Title | Open-form NavMS Sodium Channel Pore (with C-terminal Domain) after thallium soak | ||||||
Components | ION TRANSPORT PROTEINIon transporter | ||||||
Keywords | TRANSPORT PROTEIN / SODIUM CHANNEL / SELECTIVITY FILTER / MEMBRANE PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | MAGNETOCOCCUS MARINUS MC-1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.664 Å | ||||||
Authors | Bagneris, C. / Naylor, C.E. / Wallace, B.A. | ||||||
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.M. / 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 | 4cbc.cif.gz | 170.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cbc.ent.gz | 136.5 KB | Display | PDB format |
PDBx/mmJSON format | 4cbc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/4cbc ftp://data.pdbj.org/pub/pdb/validation_reports/cb/4cbc | HTTPS FTP |
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-Related structure data
Related structure data | 4oxsC 4p2zC 4p30C 4p9oC 4p9pC 4pa3C 4pa4C 4pa6C 4pa7C 4pa9C 4bha 4cal 4cbd 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 16836.502 Da / Num. of mol.: 4 / Fragment: PORE AND CTD, RESIDUES 130-274 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MAGNETOCOCCUS MARINUS MC-1 (bacteria) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: A0L5S6 #2: Chemical | ChemComp-2CV / #3: Chemical | ChemComp-NA / #4: Water | ChemComp-HOH / | Sequence details | CONSTRUCT CONSISTS OF PORE AND C-TERMINAL DOMAIN ONLY | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 7.5 Å3/Da / Density % sol: 83.5 % / Description: NONE |
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Crystal grow | pH: 8 / Details: 0.1 M NA3CITRATE, 0.1 M TRIS, PH 8.0, 34% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97572 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2012 / Details: MIRRORS |
Radiation | Monochromator: SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97572 Å / Relative weight: 1 |
Reflection | Resolution: 2.67→45.47 Å / Num. obs: 30860 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 19.7 % / Biso Wilson estimate: 28.9 Å2 / Rmerge(I) obs: 0.3 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.67→2.79 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.7 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4BHA 4bha Resolution: 2.664→45.469 Å / SU ML: 0.32 / σ(F): 1.34 / Phase error: 34.16 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.17 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.664→45.469 Å
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Refine LS restraints |
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LS refinement shell |
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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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