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Yorodumi- PDB-6emi: Crystal structure of a variant of human butyrylcholinesterase exp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6emi | ||||||
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Title | Crystal structure of a variant of human butyrylcholinesterase expressed in bacteria. | ||||||
Components | Cholinesterase | ||||||
Keywords | HYDROLASE / alpha-beta hydrolase / prokaryotic expression / dimeric form / disulfide bond. | ||||||
Function / homology | Function and homology information cholinesterase / cocaine metabolic process / neuroblast differentiation / Neurotransmitter clearance / cholinesterase activity / response to folic acid / choline binding / response to alkaloid / acetylcholine catabolic process / negative regulation of synaptic transmission ...cholinesterase / cocaine metabolic process / neuroblast differentiation / Neurotransmitter clearance / cholinesterase activity / response to folic acid / choline binding / response to alkaloid / acetylcholine catabolic process / negative regulation of synaptic transmission / peptide hormone processing / choline metabolic process / hydrolase activity, acting on ester bonds / acetylcholinesterase activity / Aspirin ADME / nuclear envelope lumen / Synthesis of PC / Synthesis, secretion, and deacylation of Ghrelin / catalytic activity / response to glucocorticoid / xenobiotic metabolic process / learning / amyloid-beta binding / blood microparticle / negative regulation of cell population proliferation / endoplasmic reticulum lumen / enzyme binding / extracellular space / extracellular region / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.476 Å | ||||||
Authors | Brazzolotto, X. / Igert, A. / Guillon, V. / Santoni, G. / Nachon, F. | ||||||
Funding support | France, 1items
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Citation | Journal: Molecules / Year: 2017 Title: Bacterial Expression of Human Butyrylcholinesterase as a Tool for Nerve Agent Bioscavengers Development. Authors: Brazzolotto, X. / Igert, A. / Guillon, V. / Santoni, G. / Nachon, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6emi.cif.gz | 234.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6emi.ent.gz | 187 KB | Display | PDB format |
PDBx/mmJSON format | 6emi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/em/6emi ftp://data.pdbj.org/pub/pdb/validation_reports/em/6emi | HTTPS FTP |
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-Related structure data
Related structure data | 1p0iS S: Starting model for refinement |
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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, 2 molecules AB
#1: Protein | Mass: 60129.930 Da / Num. of mol.: 2 Mutation: -3G, -2A, -1M, A7T, S48P, D54G, C66M, Q71T, L110M, I111V, H126P, Q176K, K180D, N188D, K190N, S191R, S215P, F227A, T234M, L236P, Y237E, T250L, L274D, G283S, I305T, N342D, I356V, G360N, ...Mutation: -3G, -2A, -1M, A7T, S48P, D54G, C66M, Q71T, L110M, I111V, H126P, Q176K, K180D, N188D, K190N, S191R, S215P, F227A, T234M, L236P, Y237E, T250L, L274D, G283S, I305T, N342D, I356V, G360N, V377E, D379E, Q380D, E387D, G390A, D391E, N397F, T406A, F409Y, S410A, W412H, F417Y, D454L, A459E, S466E, V468M, K469R, S489Q, S495P, T508S, Q518H, T523N, 530STOP Source method: isolated from a genetically manipulated source Details: A and B chains were numbered according to the sequence of the physiological human butyrylcholinaesterase. Source: (gene. exp.) Homo sapiens (human) / Gene: BCHE, CHE1 / Production host: Escherichia coli (E. coli) / References: UniProt: P06276, cholinesterase |
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-Non-polymers , 6 types, 415 molecules
#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-PEG / #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-PGE / #6: Chemical | #7: 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: 3.04 Å3/Da / Density % sol: 59.59 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.074 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 27, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.074 Å / Relative weight: 1 |
Reflection | Resolution: 2.476→65.02 Å / Num. obs: 51072 / % possible obs: 98.37 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.1163 / Rpim(I) all: 0.0737 / Rrim(I) all: 0.1381 / Net I/σ(I): 7.92 |
Reflection shell | Resolution: 2.476→2.565 Å / Rmerge(I) obs: 0.5303 / Rpim(I) all: 0.3278 / Rrim(I) all: 0.6246 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1P0I Resolution: 2.476→65.02 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.19 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.476→65.02 Å
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Refine LS restraints |
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LS refinement shell |
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