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Yorodumi- PDB-4aqd: Crystal structure of fully glycosylated human butyrylcholinesterase -
+Open data
-Basic information
Entry | Database: PDB / ID: 4aqd | |||||||||
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Title | Crystal structure of fully glycosylated human butyrylcholinesterase | |||||||||
Components | BUTYRYLCHOLINESTERASE | |||||||||
Keywords | HYDROLASE / ACETYLCHOLINESTERASE / EXPRESSION / HUPRINE / SERINE HYDROLASE / CATALYTIC TRIAD / INSECT CELLS / GLYCOSYLATIONS | |||||||||
Function / homology | Function and homology information cholinesterase / cocaine metabolic process / neuroblast differentiation / Neurotransmitter clearance / choline metabolic process / response to alkaloid / choline binding / response to folic acid / acetylcholine catabolic process / negative regulation of synaptic transmission ...cholinesterase / cocaine metabolic process / neuroblast differentiation / Neurotransmitter clearance / choline metabolic process / response to alkaloid / choline binding / response to folic acid / acetylcholine catabolic process / negative regulation of synaptic transmission / cholinesterase activity / peptide hormone processing / acetylcholinesterase activity / hydrolase activity, acting on ester bonds / nuclear envelope lumen / Aspirin ADME / Synthesis of PC / Synthesis, secretion, and deacylation of Ghrelin / catalytic activity / response to glucocorticoid / xenobiotic metabolic process / learning / amyloid-beta binding / blood microparticle / endoplasmic reticulum lumen / negative regulation of cell population proliferation / 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: 2.5 Å | |||||||||
Authors | Brazzolotto, X. / Wandhammer, M. / Ronco, C. / Trovaslet, M. / Jean, L. / Lockridge, O. / Renard, P.Y. / Nachon, F. | |||||||||
Citation | Journal: FEBS J. / Year: 2012 Title: Human butyrylcholinesterase produced in insect cells: huprine-based affinity purification and crystal structure. Authors: Brazzolotto, X. / Wandhammer, M. / Ronco, C. / Trovaslet, M. / Jean, L. / Lockridge, O. / Renard, P.Y. / Nachon, F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4aqd.cif.gz | 453.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4aqd.ent.gz | 373.8 KB | Display | PDB format |
PDBx/mmJSON format | 4aqd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aq/4aqd ftp://data.pdbj.org/pub/pdb/validation_reports/aq/4aqd | 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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2 |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 59901.672 Da / Num. of mol.: 2 / Fragment: RESIDUES 27-557 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PMT-BIP / Cell line (production host): S2 / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: P06276, cholinesterase |
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-Sugars , 4 types, 15 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #4: Polysaccharide | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-NAG / |
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-Non-polymers , 8 types, 322 molecules
#5: Chemical | #7: Chemical | #8: Chemical | ChemComp-EDO / #9: Chemical | ChemComp-UNX / #10: Chemical | ChemComp-CL / #11: Chemical | #12: Chemical | #13: 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: 2.7 Å3/Da / Density % sol: 55 % / Description: NONE |
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Crystal grow | Temperature: 293 K / pH: 7.4 Details: PROTEIN WAS CRYSTALLIZED FROM 20% PEG 3350, 0.2 M NH4OAC PH 7.4, AT 293 K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97939 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 8, 2011 |
Radiation | Monochromator: SILICON (1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97939 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→39 Å / Num. obs: 46071 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 46.58 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.3 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 3.3 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1P0I Resolution: 2.5→39.041 Å / SU ML: 0.35 / σ(F): 1.36 / Phase error: 22.76 / Stereochemistry target values: ML Details: A BETA-ALANINE WAS MODELED AT BOND DISTANCE TO THE CATALYTIC SERINE. A PEAK OF ELECTRON DENSITY CLOSE TO A PEAK OF ELECTRON DENSITY CLOSE TO TRP82 WAS MODELED AS DUMMY ATOMS (RESIDUES UNX).
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.675 Å2 / ksol: 0.362 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.5→39.041 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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