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- PDB-8d8x: Crystal structure of ChoE in complex with acetate and thiocholine... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8d8x | ||||||
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Title | Crystal structure of ChoE in complex with acetate and thiocholine (crystal form 2) | ||||||
![]() | ChoE | ||||||
![]() | HYDROLASE / esterase | ||||||
Function / homology | GDSL lipase/esterase / GDSL-like Lipase/Acylhydrolase / SGNH hydrolase superfamily / cholinesterase activity / Prokaryotic membrane lipoprotein lipid attachment site profile. / extracellular region / ACETATE ION / 2-(TRIMETHYLAMMONIUM)ETHYL THIOL / ChoE![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pham, V.D. / Shi, R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structures of bacterial acetylcholinesterase ChoE provide insights into the plasticity of catalytic Ser in regulating the active site geometry and the functional state of the SGNH hydrolases Authors: Pham, V.D. / Couture, M. / Lortie, L.-A. / Picard, M.-E. / Charette, S. / Levesque, R. / Shi, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 84.8 KB | Display | ![]() |
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PDB format | ![]() | 60 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 18.3 KB | Display | |
Data in CIF | ![]() | 28.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8d8wC ![]() 8d8yC ![]() 8d8zC ![]() 8d90C ![]() 8d91C ![]() 6uqvS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 31543.293 Da / Num. of mol.: 1 / Fragment: UNP residues 21-307 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: choE, PA4921 / Plasmid: pET28a / Production host: ![]() ![]() |
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-Non-polymers , 6 types, 411 molecules ![](data/chem/img/ACT.gif)
![](data/chem/img/ETM.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ETM.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ACT / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Chemical | ChemComp-CL / | #6: Chemical | ChemComp-P6G / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.5 % / Mosaicity: 0.11 ° |
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Crystal grow | Temperature: 277 K / Method: microbatch / pH: 6.5 / Details: 25% PEG 8000, 0.1M MES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 19, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.36→65.973 Å / Num. all: 82313 / Num. obs: 82313 / % possible obs: 99.9 % / Redundancy: 13.1 % / Rpim(I) all: 0.023 / Rrim(I) all: 0.083 / Rsym value: 0.08 / Net I/av σ(I): 6.8 / Net I/σ(I): 18.5 / Num. measured all: 1082293 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6UQV Resolution: 1.36→46.2 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.896 / SU ML: 0.035 / SU R Cruickshank DPI: 0.0445 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.045 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 86.02 Å2 / Biso mean: 18.957 Å2 / Biso min: 8.61 Å2
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Refinement step | Cycle: final / Resolution: 1.36→46.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.36→1.395 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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