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- PDB-6ur1: Crystal structure of ChoE S38A mutant in complex with acetate and... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ur1 | ||||||
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Title | Crystal structure of ChoE S38A mutant in complex with acetate and acetylthiocholine | ||||||
![]() | ChoE![]() | ||||||
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Function / homology | GDSL lipase/esterase / GDSL-like Lipase/Acylhydrolase / SGNH hydrolase superfamily / ![]() ![]() ![]() ![]() ![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pham, V.D. / Shi, R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into the putative bacterial acetylcholinesterase ChoE and its substrate inhibition mechanism. Authors: Pham, V.D. / To, T.A. / Gagne-Thivierge, C. / Couture, M. / Lague, P. / Yao, D. / Picard, M.E. / Lortie, L.A. / Attere, S.A. / Zhu, X. / Levesque, R.C. / Charette, S.J. / 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 | ![]() | 143.2 KB | Display | ![]() |
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PDB format | ![]() | 109.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6uqvSC ![]() 6uqwC ![]() 6uqxC ![]() 6uqyC ![]() 6uqzC ![]() 6ur0C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 31527.293 Da / Num. of mol.: 2 / Fragment: UNP residues 21-307 / Mutation: S38A 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: ![]() ![]() ![]() #2: Chemical | ![]() #3: Chemical | ![]() #4: Chemical | ![]() #5: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.85 % / Mosaicity: 0.13 ° |
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Crystal grow![]() | Temperature: 277 K / Method: microbatch / pH: 6.5 / Details: 15% PEG20000, 0.1 M 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 | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.42→80.078 Å / Num. all: 106729 / Num. obs: 106729 / % possible obs: 97 % / Redundancy: 3.4 % / Rpim(I) all: 0.024 / Rrim(I) all: 0.044 / Rsym value: 0.037 / Net I/av σ(I): 13.6 / Net I/σ(I): 17 / Num. measured all: 365050 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 6UQV Resolution: 1.42→44.89 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / WRfactor Rfree: 0.1886 / WRfactor Rwork: 0.1568 / FOM work R set: 0.8263 / SU B: 1.342 / SU ML: 0.05 / SU R Cruickshank DPI: 0.061 / SU Rfree: 0.0643 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.064 / 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: 71.41 Å2 / Biso mean: 21.042 Å2 / Biso min: 8.4 Å2
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Refinement step | Cycle: final / Resolution: 1.42→44.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.42→1.457 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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