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Yorodumi- PDB-4axb: Crystal structure of soman-aged human butyrylcholinesterase in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4axb | |||||||||
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Title | Crystal structure of soman-aged human butyrylcholinesterase in complex with 2-PAM | |||||||||
Components | CHOLINESTERASE | |||||||||
Keywords | HYDROLASE / AGING | |||||||||
Function / homology | Function and homology information cholinesterase / cocaine metabolic process / neuroblast differentiation / Neurotransmitter clearance / choline metabolic process / choline binding / response to folic acid / response to alkaloid / acetylcholine catabolic process / negative regulation of synaptic transmission ...cholinesterase / cocaine metabolic process / neuroblast differentiation / Neurotransmitter clearance / choline metabolic process / choline binding / response to folic acid / response to alkaloid / 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 / 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: 2.4 Å | |||||||||
Authors | Wandhammer, M. / de Koning, M. / Noort, D. / Goeldner, M. / Nachon, F. | |||||||||
Citation | Journal: Chem.Biol.Interact / Year: 2013 Title: A Step Toward the Reactivation of Aged Cholinesterases -Crystal Structure of Ligands Binding to Aged Human Butyrylcholinesterase Authors: Wandhammer, M. / De Koning, M. / Van Grol, M. / Loiodice, M. / Saurel, L. / Noort, D. / Goeldner, M. / Nachon, F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4axb.cif.gz | 246.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4axb.ent.gz | 198.7 KB | Display | PDB format |
PDBx/mmJSON format | 4axb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/4axb ftp://data.pdbj.org/pub/pdb/validation_reports/ax/4axb | HTTPS FTP |
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-Related structure data
Related structure data | 4b0oC 4b0pC 1p0iS 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 59547.316 Da / Num. of mol.: 1 / Fragment: RESIDUES 31-557 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGS / Cell line (production host): CHO K1 / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: P06276, cholinesterase |
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-Sugars , 2 types, 6 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #8: Sugar | ChemComp-NAG / |
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-Non-polymers , 6 types, 367 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-FP1 / | #9: 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: 3.09 Å3/Da / Density % sol: 60.14 % / Description: NONE |
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Crystal grow | pH: 7.4 Details: PROTEIN WAS CRYSTALLIZED FROM 2.1 M AMMONIUM SULFATE, 100 MM MES BUFFER PH 6.5. THEN SOAKED IN 20% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 63 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 13, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→110.27 Å / Num. obs: 29874 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 8.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.4→2.55 Å / Redundancy: 9 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 5.2 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1P0I Resolution: 2.4→110.27 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.931 / SU B: 13.254 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.281 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.713 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→110.27 Å
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