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Open data
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Basic information
Entry | Database: PDB / ID: 4lmj | ||||||
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Title | GLIC Liganded-closed-channel Conformation, Mutant T25'A | ||||||
![]() | Proton-gated ion channel | ||||||
![]() | TRANSPORT PROTEIN / pentameric ligand-gated ion channel / membrane protein / prokaryotic CYS-loop receptor | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Grosman, C. / Gonzalez-Gutierrez, G. | ||||||
![]() | ![]() Title: Gating of the proton-gated ion channel from Gloeobacter violaceus at pH 4 as revealed by X-ray crystallography. Authors: Gonzalez-Gutierrez, G. / Cuello, L.G. / Nair, S.K. / Grosman, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 314.7 KB | Display | ![]() |
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PDB format | ![]() | 258.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 483.2 KB | Display | ![]() |
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Full document | ![]() | 514.8 KB | Display | |
Data in XML | ![]() | 53.3 KB | Display | |
Data in CIF | ![]() | 72.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4lmkC ![]() 4lmlC ![]() 3ehzS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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: PRO / Beg label comp-ID: PRO / End auth comp-ID: PHE / End label comp-ID: PHE / Auth seq-ID: 7 - 316 / Label seq-ID: 9 - 318
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Components
#1: Protein | Mass: 36334.781 Da / Num. of mol.: 5 / Fragment: UNP residues 44-359 / Mutation: T291A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CL / #3: Sugar | ChemComp-LMT / | #4: Chemical | ChemComp-NA / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.24 Å3/Da / Density % sol: 76.5 % Description: RPIM = 0.095 (0.453 FOR HIGHEST RESOLUTION SHELL) |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 10-12% PEG4000, 225 mM ammonium sulfate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 20, 2012 |
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 3.44→49.04 Å / Num. obs: 41437 / % possible obs: 98.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 51.8 Å2 / Rmerge(I) obs: 0.156 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 3.44→3.56 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.749 / Mean I/σ(I) obs: 1.4 / % possible all: 92.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3EHZ Resolution: 3.44→49.038 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.41 / σ(F): 0.12 / Phase error: 28.63 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.3174 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.44→49.038 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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