[English] 日本語
Yorodumi- PDB-6uqz: Crystal structure of ChoE D285N mutant in complex with acetate an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6uqz | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of ChoE D285N mutant in complex with acetate and thiocholine | ||||||
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 / ACETATE ION / 2-(TRIMETHYLAMMONIUM)ETHYL THIOL / ChoE Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å | ||||||
Authors | Pham, V.D. / Shi, R. | ||||||
Funding support | Canada, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6uqz.cif.gz | 141.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6uqz.ent.gz | 107.8 KB | Display | PDB format |
PDBx/mmJSON format | 6uqz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6uqz_validation.pdf.gz | 335.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6uqz_full_validation.pdf.gz | 335.2 KB | Display | |
Data in XML | 6uqz_validation.xml.gz | 1.4 KB | Display | |
Data in CIF | 6uqz_validation.cif.gz | 10.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uq/6uqz ftp://data.pdbj.org/pub/pdb/validation_reports/uq/6uqz | HTTPS FTP |
-Related structure data
Related structure data | 6uqvSC 6uqwC 6uqxC 6uqyC 6ur0C 6ur1C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 31542.309 Da / Num. of mol.: 2 / Fragment: UNP residues 21-307 / Mutation: D285N 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 | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.01 % / Mosaicity: 0.16 ° |
---|---|
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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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: 1.43→80.17 Å / Num. obs: 104293 / % possible obs: 96.4 % / Redundancy: 3.4 % / Rpim(I) all: 0.03 / Rrim(I) all: 0.056 / Rsym value: 0.047 / Net I/av σ(I): 9.9 / Net I/σ(I): 13.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6UQV Resolution: 1.43→80.17 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.467 / SU ML: 0.054 / SU R Cruickshank DPI: 0.0648 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.067 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 72.69 Å2 / Biso mean: 20.865 Å2 / Biso min: 8.55 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.43→80.17 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.43→1.467 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|