[English] 日本語
Yorodumi- PDB-3uu6: The GLIC pentameric Ligand-Gated Ion Channel Loop2-22' mutant red... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3uu6 | ||||||
---|---|---|---|---|---|---|---|
Title | The GLIC pentameric Ligand-Gated Ion Channel Loop2-22' mutant reduced in solution | ||||||
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 transporter complex / regulation of membrane potential / transmembrane signaling receptor activity / neuron projection / signal transduction / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Gloeobacter violaceus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 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 | 3uu6.cif.gz | 328.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3uu6.ent.gz | 266.2 KB | Display | PDB format |
PDBx/mmJSON format | 3uu6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3uu6_validation.pdf.gz | 3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3uu6_full_validation.pdf.gz | 3.1 MB | Display | |
Data in XML | 3uu6_validation.xml.gz | 59.7 KB | Display | |
Data in CIF | 3uu6_validation.cif.gz | 79 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uu/3uu6 ftp://data.pdbj.org/pub/pdb/validation_reports/uu/3uu6 | HTTPS FTP |
-Related structure data
Related structure data | 3tlsC 3tltC 3tluC 3tlvC 3tlwC 3uu3C 3uu4C 3uu5C 3uu8C 3uubC 3eamS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein / Sugars , 2 types, 11 molecules ABCDE
#1: Protein | Mass: 36525.922 Da / Num. of mol.: 5 / Fragment: UNP residues 44-359 / Mutation: C27S,K33C,L246C 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 #4: Sugar | ChemComp-LMT / |
---|
-Non-polymers , 4 types, 90 molecules
#2: Chemical | ChemComp-PLC / #3: Chemical | ChemComp-CL / #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 5.14 Å3/Da / Density % sol: 76.09 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 15% PEG4000, 0.4 M sodium thiocyanate, 0.1 M sodium acetate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9537 Å | ||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2011 | ||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.98→49.5 Å / Num. all: 75054 / Num. obs: 74738 / % possible obs: 99.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 81.97 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.04 / Net I/σ(I): 13 | ||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 3.4 %
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3EAM Resolution: 2.98→26.65 Å / Cor.coef. Fo:Fc: 0.8346 / Cor.coef. Fo:Fc free: 0.8327 / SU R Cruickshank DPI: 0.521 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.469 / SU Rfree Blow DPI: 0.287 / SU Rfree Cruickshank DPI: 0.3
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 82.14 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.426 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.98→26.65 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.98→3.06 Å / Total num. of bins used: 20
|