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Yorodumi- PDB-4ltp: Bacterial sodium channel in high calcium, I222 space group, crystal 2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ltp | ||||||
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Title | Bacterial sodium channel in high calcium, I222 space group, crystal 2 | ||||||
Components | Ion transport protein | ||||||
Keywords | TRANSPORT PROTEIN / cation channel fold / coiled coil sodium channel / plasma membrane | ||||||
Function / homology | Function and homology information voltage-gated sodium channel complex / membrane depolarization during action potential / voltage-gated sodium channel activity / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | Alkalilimnicola ehrlichii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 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 | 4ltp.cif.gz | 118.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ltp.ent.gz | 90.9 KB | Display | PDB format |
PDBx/mmJSON format | 4ltp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ltp_validation.pdf.gz | 461.3 KB | Display | wwPDB validaton report |
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Full document | 4ltp_full_validation.pdf.gz | 488 KB | Display | |
Data in XML | 4ltp_validation.xml.gz | 24 KB | Display | |
Data in CIF | 4ltp_validation.cif.gz | 31.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lt/4ltp ftp://data.pdbj.org/pub/pdb/validation_reports/lt/4ltp | HTTPS FTP |
-Related structure data
Related structure data | 4ltoSC 4ltqC 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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1 |
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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.: 4 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 #2: Chemical | ChemComp-CA / #3: 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: 6.88 Å3/Da / Density % sol: 82.1 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 200 mM calcium chloride, 30% PEG400, 100 mM sodium acetate, pH 5.0, 0.5 M TMAO, 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: Nov 21, 2011 |
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 | Resolution: 3.8→50 Å / Num. all: 19278 / Num. obs: 19162 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Biso Wilson estimate: 143 Å2 / Rmerge(I) obs: 0.181 / Net I/σ(I): 6 |
Reflection shell | Resolution: 3.8→4.01 Å / Redundancy: 6.4 % / Rmerge(I) obs: 3.306 / Mean I/σ(I) obs: 0.5 / Num. unique all: 2683 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4LTO Resolution: 3.8→15 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.95 / SU B: 37.039 / SU ML: 0.478 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 1.378 / ESU R Free: 0.506 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 170.143 Å2
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Refinement step | Cycle: LAST / Resolution: 3.8→15 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 996 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 3
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LS refinement shell | Resolution: 3.8→3.895 Å / Total num. of bins used: 20
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