+Open data
-Basic information
Entry | Database: PDB / ID: 4ltq | ||||||
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Title | Bacterial sodium channel in low calcium, P42 space group | ||||||
Components | Ion transport proteinIon transporter | ||||||
Keywords | TRANSPORT PROTEIN / cation channel fold / coiled coil sodium channel / plasma membrane | ||||||
Function / homology | Voltage-gated cation channel calcium and sodium / Voltage-dependent channel domain superfamily / monoatomic cation channel activity / Ion transport domain / Ion transport protein / identical protein binding / metal ion binding / plasma membrane / Ion transport protein Function and homology information | ||||||
Biological species | Alkalilimnicola ehrlichii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.5 Å | ||||||
Authors | Shaya, D. / Findeisen, F. / Abderemane-Ali, F. / Arrigoni, C. / Wong, S. / Reddy Nurva, S. / Loussouarn, G. / Minor, D.L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2014 Title: Structure of a prokaryotic sodium channel pore reveals essential gating elements and an outer ion binding site common to eukaryotic channels. Authors: Shaya, D. / Findeisen, F. / Abderemane-Ali, F. / Arrigoni, C. / Wong, S. / Nurva, S.R. / Loussouarn, G. / Minor, D.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ltq.cif.gz | 213.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ltq.ent.gz | 171.4 KB | Display | PDB format |
PDBx/mmJSON format | 4ltq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lt/4ltq ftp://data.pdbj.org/pub/pdb/validation_reports/lt/4ltq | HTTPS FTP |
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-Related structure data
Related structure data | 4ltoSC 4ltpC 4ltrC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 1 / Auth seq-ID: 150 - 285 / Label seq-ID: 14 - 149
NCS oper:
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-Components
#1: Protein | Mass: 17463.344 Da / Num. of mol.: 8 Fragment: Pore and cytoplasmic domains (UNP residues 143-288) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alkalilimnicola ehrlichii (bacteria) / Gene: Mlg_0322 / Plasmid: pet24b HM3C-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q0ABW0 |
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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: 5.52 Å3/Da / Density % sol: 77.7 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 200 mM magnesium chloride, 30% PEG400, 100 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å | |||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 16, 2010 | |||||||||||||||
Radiation | Monochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 5.5→50 Å / Num. all: 10095 / Num. obs: 9811 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 307 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 9.8 | |||||||||||||||
Reflection shell | Resolution: 5.5→5.8 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.916 / Mean I/σ(I) obs: 0.7 / Num. unique all: 1236 / % possible all: 86.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4LTO Resolution: 5.5→15 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.918 / SU B: 45.904 / SU ML: 0.526 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.337 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 292.6 Å2
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Refinement step | Cycle: LAST / Resolution: 5.5→15 Å
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Refine LS restraints |
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