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Yorodumi- PDB-5ydj: Crystal structure of anopheles gambiae acetylcholinesterase in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ydj | ||||||||||||
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Title | Crystal structure of anopheles gambiae acetylcholinesterase in complex with PMSF | ||||||||||||
Components | Acetylcholinesterase | ||||||||||||
Keywords | HYDROLASE / ACETYLCHOLINESTERASE PMSF | ||||||||||||
Function / homology | Function and homology information choline metabolic process / acetylcholine catabolic process / acetylcholinesterase / acetylcholinesterase activity / synapse / extracellular space / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Anopheles gambiae (African malaria mosquito) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.04 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 | 5ydj.cif.gz | 234.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ydj.ent.gz | 184.9 KB | Display | PDB format |
PDBx/mmJSON format | 5ydj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yd/5ydj ftp://data.pdbj.org/pub/pdb/validation_reports/yd/5ydj | HTTPS FTP |
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-Related structure data
Related structure data | 5ydhC 5ydiC 5x61S 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, 2 molecules AB
#1: Protein | Mass: 81143.398 Da / Num. of mol.: 2 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 , 2 types, 4 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | |
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-Non-polymers , 3 types, 79 molecules
#4: Chemical | ChemComp-SO4 / #5: Chemical | #6: 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: 4.35 Å3/Da / Density % sol: 71.7 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES BUFFER, 1.6M AMMONIUM SULFATE, PH 7.5, 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 25, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 3.04→61.48 Å / Num. obs: 51171 / % possible obs: 100 % / Redundancy: 22.7 % / Net I/σ(I): 24.9 |
Reflection shell | Resolution: 3.04→3.12 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5X61 Resolution: 3.04→61.48 Å / Cor.coef. Fo:Fc: 0.85 / Cor.coef. Fo:Fc free: 0.804 / Cross valid method: THROUGHOUT / ESU R: 0.592 / ESU R Free: 0.37 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.244 Å2
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Refinement step | Cycle: 1 / Resolution: 3.04→61.48 Å
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Refine LS restraints |
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