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- PDB-5obg: Crystal structure of glycine binding protein in complex with stry... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5obg | ||||||
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Title | Crystal structure of glycine binding protein in complex with strychnine | ||||||
![]() | Soluble acetylcholine receptor | ||||||
![]() | SIGNALING PROTEIN / receptor / acetylcholine binding | ||||||
Function / homology | ![]() acetylcholine receptor activity / acetylcholine-gated monoatomic cation-selective channel activity / response to nicotine / neuron projection / synapse / identical protein binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Dawson, A. / Hunter, W.N. / Jones, M. | ||||||
![]() | ![]() Title: Engineering a surrogate human heteromeric alpha / beta glycine receptor orthosteric site exploiting the structural homology and stability of acetylcholine-binding protein. Authors: Dawson, A. / Trumper, P. / de Souza, J.O. / Parker, H. / Jones, M.J. / Hales, T.G. / Hunter, W.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 246 KB | Display | ![]() |
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PDB format | ![]() | 197.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.5 MB | Display | ![]() |
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Full document | ![]() | 2.5 MB | Display | |
Data in XML | ![]() | 51.1 KB | Display | |
Data in CIF | ![]() | 71.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5o87C ![]() 5o8tC ![]() 5oa0C ![]() 5oadC ![]() 5oajC ![]() 5oalC ![]() 5oanSC S: Starting model for refinement C: citing same article ( |
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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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Components
-Protein / Sugars , 2 types, 9 molecules ABCDE![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: Protein | Mass: 28309.680 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() #6: Sugar | ChemComp-NAG / |
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-Non-polymers , 5 types, 799 molecules ![](data/chem/img/SY9.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SY9 / #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-ACT / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.95 % / Description: block |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Reservoir buffer: 20 % PEG 3350, 0.2 M MgOAc Protein buffer: 50 mM tris, 250 mM NaCl, pH 7.5, 0.5 mM strychnine |
-Data collection
Diffraction | Mean temperature: 150 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 11, 2017 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54157 Å / Relative weight: 1 |
Reflection | Resolution: 2→47.92 Å / Num. obs: 100843 / % possible obs: 100 % / Redundancy: 6.2 % / Biso Wilson estimate: 19 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.147 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4919 / CC1/2: 0.657 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5oan Resolution: 2→47.92 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.912 / SU B: 4.859 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.16 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.39 Å2
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Refinement step | Cycle: 1 / Resolution: 2→47.92 Å
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Refine LS restraints |
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