[English] 日本語
Yorodumi- PDB-3tlv: The GLIC pentameric Ligand-Gated Ion Channel Loop2-22' oxidized m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tlv | ||||||
---|---|---|---|---|---|---|---|
Title | The GLIC pentameric Ligand-Gated Ion Channel Loop2-22' oxidized mutant in a locally-closed conformation (LC3 subtype) | ||||||
Components | Glr4197 protein | ||||||
Keywords | MEMBRANE PROTEIN / TRANSPORT PROTEIN / Cys-loop receptor family | ||||||
Function / homology | Function and homology information sodium channel activity / extracellular ligand-gated monoatomic ion channel activity / potassium channel activity / transmembrane signaling receptor activity / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Gloeobacter violaceus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Sauguet, L. / Nury, H. / Corringer, P.J. / Delarue, M. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2012 Title: A locally closed conformation of a bacterial pentameric proton-gated ion channel. Authors: Prevost, M.S. / Sauguet, L. / Nury, H. / Van Renterghem, C. / Huon, C. / Poitevin, F. / Baaden, M. / Delarue, M. / Corringer, P.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3tlv.cif.gz | 309.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3tlv.ent.gz | 263.6 KB | Display | PDB format |
PDBx/mmJSON format | 3tlv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tl/3tlv ftp://data.pdbj.org/pub/pdb/validation_reports/tl/3tlv | HTTPS FTP |
---|
-Related structure data
Related structure data | 3tlsC 3tltC 3tluC 3tlwC 3uu3C 3uu4C 3uu5C 3uu6C 3uu8C 3uubC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 36525.922 Da / Num. of mol.: 5 / Fragment: UNP residues 44-359 / Mutation: C69S/K75C/L288C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gloeobacter violaceus (bacteria) / Gene: glr4197 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7NDN8 #2: Sugar | ChemComp-LMT / | #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.94 Å3/Da / Density % sol: 75.09 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 4 / Details: pH 4, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 |
---|---|
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Monochromator: channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.9→49.23 Å / Num. obs: 78570 / % possible obs: 99.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 80.19 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.042 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.9→3.05 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.677 / Mean I/σ(I) obs: 2 / Num. unique all: 11073 / Rsym value: 0.395 / % possible all: 96.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→49.23 Å / Cor.coef. Fo:Fc: 0.8401 / Cor.coef. Fo:Fc free: 0.8366 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.424 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.387 / SU Rfree Blow DPI: 0.255 / SU Rfree Cruickshank DPI: 0.267
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 184.35 Å2 / Biso mean: 78.0608 Å2 / Biso min: 30.16 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.385 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→49.23 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.9→2.98 Å / Total num. of bins used: 20
|