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Yorodumi- PDB-6uqy: Crystal structure of ChoE H288N mutant in complex with acetylthio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6uqy | ||||||
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Title | Crystal structure of ChoE H288N mutant in complex with acetylthiocholine | ||||||
Components | ChoE | ||||||
Keywords | 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 / ACETYLTHIOCHOLINE / ChoE Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å | ||||||
Authors | Pham, V.D. / Shi, R. | ||||||
Funding support | Canada, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6uqy.cif.gz | 140.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6uqy.ent.gz | 107.3 KB | Display | PDB format |
PDBx/mmJSON format | 6uqy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6uqy_validation.pdf.gz | 353.2 KB | Display | wwPDB validaton report |
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Full document | 6uqy_full_validation.pdf.gz | 354 KB | Display | |
Data in XML | 6uqy_validation.xml.gz | 1.7 KB | Display | |
Data in CIF | 6uqy_validation.cif.gz | 11 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uq/6uqy ftp://data.pdbj.org/pub/pdb/validation_reports/uq/6uqy | HTTPS FTP |
-Related structure data
Related structure data | 6uqvSC 6uqwC 6uqxC 6uqzC 6ur0C 6ur1C 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
#1: Protein | Mass: 31519.250 Da / Num. of mol.: 2 / Fragment: UNP residues 21-307 / Mutation: H288N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: choE, PA4921 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q9HUP2, Hydrolases; Acting on ester bonds #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.37 Å3/Da / Density % sol: 48.04 % / Mosaicity: 0.24 ° |
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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: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 8, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.57→80.26 Å / Num. all: 79982 / Num. obs: 79982 / % possible obs: 97.7 % / Redundancy: 6.7 % / Rpim(I) all: 0.025 / Rrim(I) all: 0.067 / Rsym value: 0.061 / Net I/av σ(I): 10 / Net I/σ(I): 16.9 / Num. measured all: 538220 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6UQV Resolution: 1.57→36.57 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.857 / SU ML: 0.062 / SU R Cruickshank DPI: 0.0752 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.077 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.05 Å2 / Biso mean: 25.123 Å2 / Biso min: 12.97 Å2
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Refinement step | Cycle: final / Resolution: 1.57→36.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.57→1.611 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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