+Open data
-Basic information
Entry | Database: PDB / ID: 3sh1 | |||||||||
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Title | Ac-AChBP ligand binding domain mutated to human alpha-7 nAChR | |||||||||
Components | Soluble acetylcholine receptor | |||||||||
Keywords | RECEPTOR / Human nicotinic acetylcholine receptor binding protein / Methyllycaconitine Binding / Glycosylation | |||||||||
Function / homology | Function and homology information extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / membrane / identical protein binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Aplysia californica (California sea hare) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | |||||||||
Authors | Nemecz, A. / Taylor, P.W. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Creating an alpha-7 nicotinic acetylcholine recognition domain from the acetylcholine binding protein: crystallographic and ligand selectivity analyses Authors: Nemecz, A. / Taylor, P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3sh1.cif.gz | 458.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sh1.ent.gz | 380.9 KB | Display | PDB format |
PDBx/mmJSON format | 3sh1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sh/3sh1 ftp://data.pdbj.org/pub/pdb/validation_reports/sh/3sh1 | HTTPS FTP |
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-Related structure data
Related structure data | 3sioC 3t4mC 2byrS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 10 molecules ABCDEFGHIJ
#1: Protein | Mass: 26323.051 Da / Num. of mol.: 10 / Fragment: unp entry 18-236 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aplysia californica (California sea hare) Gene: LOC100533247 soluble acetylcholine receptor / Plasmid: pFlag-CMV3 / Cell line (production host): HEK293S Gnt1- / Production host: Homo sapiens (human) / References: UniProt: Q8WSF8 |
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-Sugars , 3 types, 13 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #8: Sugar | ChemComp-NAG / |
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-Non-polymers , 6 types, 99 molecules
#4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-MLK / #6: Chemical | ChemComp-MRD / ( #7: Chemical | ChemComp-MPD / ( #9: Chemical | ChemComp-ACT / | #10: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.22 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30%MPD, 0.1M Na Cacodylate, 0.2M Magnesium Acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 3, 2011 |
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 85106 / % possible obs: 73.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Rmerge(I) obs: 0.138 / Rsym value: 0.138 / Net I/σ(I): 13.909 |
Reflection shell | Resolution: 2.9→2.95 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.952 / Mean I/σ(I) obs: 1.5 / Rsym value: 0 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Modified via pymol PDB entry 2BYR Resolution: 2.9→48.054 Å / SU ML: 0.38 / Isotropic thermal model: Isotropic / σ(F): 0.19 / Phase error: 28.89 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.137 Å2 / ksol: 0.303 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.9→48.054 Å
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Refine LS restraints |
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LS refinement shell |
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