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Yorodumi- PDB-5ydi: Crystal structure of acetylcholinesterase catalytic subunits of t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ydi | |||||||||
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Title | Crystal structure of acetylcholinesterase catalytic subunits of the malaria vector anopheles gambiae, new crystal packing | |||||||||
Components | Acetylcholinesterase | |||||||||
Keywords | HYDROLASE / ALPHA/BATA HYDROLASE | |||||||||
Function / homology | Function and homology information acetylcholine catabolic process / acetylcholinesterase / acetylcholinesterase activity / choline metabolic process / synapse / extracellular space / plasma membrane Similarity search - Function | |||||||||
Biological species | Anopheles gambiae (African malaria mosquito) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 Å | |||||||||
Authors | Han, Q. / Guan, H. / Ding, H. / Liao, C. / Robinson, H. / Li, J. | |||||||||
Funding support | China, United States, 2items
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Citation | Journal: To Be Published Title: Crystal structures of acetylcholinesterase of the malaria vector Anopheles gambiae reveal a polymerization interface, ligand binding residues and post translational modifications Authors: Han, Q. / Guan, H. / Ding, H. / Liao, C. / Robinson, H. / Li, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ydi.cif.gz | 325 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ydi.ent.gz | 263.7 KB | Display | PDB format |
PDBx/mmJSON format | 5ydi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ydi_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 5ydi_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 5ydi_validation.xml.gz | 56.8 KB | Display | |
Data in CIF | 5ydi_validation.cif.gz | 76.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yd/5ydi ftp://data.pdbj.org/pub/pdb/validation_reports/yd/5ydi | HTTPS FTP |
-Related structure data
Related structure data | 5ydhSC 5ydjC 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, 3 molecules ABC
#1: Protein | Mass: 61684.125 Da / Num. of mol.: 3 / Fragment: CATALYTIC SUBUNIT, UNP RESIDUES 162-714 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anopheles gambiae (African malaria mosquito) Gene: Ace, ACE1, ACHE1, AGAP001356 / Plasmid: PPICZ*A / Production host: Komagataella pastoris (fungus) / References: UniProt: Q869C3, acetylcholinesterase |
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-Sugars , 3 types, 6 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-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 #4: Sugar | |
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-Non-polymers , 3 types, 18 molecules
#5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-NA / #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: 3.4 Å3/Da / Density % sol: 63.79 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES BUFFER, 20% PEG 4000, 22% GLYCEROL, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 28, 2013 |
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 3.45→63.72 Å / Num. obs: 31768 / % possible obs: 76 % / Observed criterion σ(I): -3 / Redundancy: 13.1 % / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 3.45→3.64 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5YDH Resolution: 3.45→63.72 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.854 / SU B: 25.984 / SU ML: 0.404 / Cross valid method: THROUGHOUT / ESU R Free: 0.543
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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: 62.64 Å2
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Refinement step | Cycle: LAST / Resolution: 3.45→63.72 Å
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Refine LS restraints |
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