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- PDB-3igq: Crystal structure of the extracellular domain of a bacterial pent... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3igq | ||||||
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Title | Crystal structure of the extracellular domain of a bacterial pentameric ligand-gated ion channel | ||||||
![]() | Glr4197 protein | ||||||
![]() | MEMBRANE PROTEIN / TRANSPORT PROTEIN / pLGIC cys-loop | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nury, H. / Delarue, M. | ||||||
![]() | ![]() Title: Crystal structure of the extracellular domain of a bacterial ligand-gated ion channel Authors: Nury, H. / Bocquet, N. / Le Poupon, C. / Raynal, B. / Haouz, A. / Corringer, P.-J. / Delarue, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 231.5 KB | Display | ![]() |
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PDB format | ![]() | 186.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 504.7 KB | Display | ![]() |
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Full document | ![]() | 528.5 KB | Display | |
Data in XML | ![]() | 45.7 KB | Display | |
Data in CIF | ![]() | 63.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 22872.697 Da / Num. of mol.: 6 Fragment: extracellular N-terminal fragment, UNP residues 44-235 Mutation: F116G, Y119T, P120E, F121S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 432 molecules ![](data/chem/img/ACY.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ACY / #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-HG / #5: Chemical | ChemComp-CL / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 45.96 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 24, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→25 Å / Num. all: 108138 / Num. obs: 105975 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.03 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 11.23 |
Reflection shell | Resolution: 2.3→2.44 Å / Redundancy: 2.01 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 1.96 / % possible all: 97.91 |
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Processing
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Refinement | Method to determine structure: ![]() Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.Friedel's pair are not merged during data collection (the anomalous information from the mercury ions were used), while the refinement ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.Friedel's pair are not merged during data collection (the anomalous information from the mercury ions were used), while the refinement is made with merged plus and minus reflections.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.431 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→25 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.3→2.359 Å / Total num. of bins used: 20
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