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- PDB-8uqz: Round 18 Arylesterase Variant of Phosphotriesterase Bound to Gado... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8uqz | ||||||
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Title | Round 18 Arylesterase Variant of Phosphotriesterase Bound to Gadolinium(III) Measured at 9.5 keV | ||||||
![]() | Phosphotriesterase variant PTE-R18 | ||||||
![]() | HYDROLASE / Phosphotriesterase / 9.5 keV / Gadolinium | ||||||
Function / homology | ![]() catabolic process / hydrolase activity, acting on ester bonds / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Breeze, C.W. / Frkic, R.L. / Campbell, E.C. / Jackson, C.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Mononuclear binding and catalytic activity of europium(III) and gadolinium(III) at the active site of the model metalloenzyme phosphotriesterase. Authors: Breeze, C.W. / Nakano, Y. / Campbell, E.C. / Frkic, R.L. / Lupton, D.W. / Jackson, C.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 381.9 KB | Display | ![]() |
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PDB format | ![]() | 316.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 955.6 KB | Display | ![]() |
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Full document | ![]() | 960.2 KB | Display | |
Data in XML | ![]() | 27.7 KB | Display | |
Data in CIF | ![]() | 39.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8uqwC ![]() 8uqxC ![]() 8uqyC 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
#1: Protein | Mass: 36208.414 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-MPD / ( #3: Chemical | ChemComp-GD3 / | #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: 2.27 Å3/Da / Density % sol: 45.93 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 100 mM Sodium cacodylate, 14% (v/v) MPD, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 21, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3051 Å / Relative weight: 1 |
Reflection | Resolution: 1.61→44.62 Å / Num. obs: 84562 / % possible obs: 98.3 % / Redundancy: 40 % / CC1/2: 0.999 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.021 / Rrim(I) all: 0.133 / Χ2: 1.03 / Net I/σ(I): 21.2 / Num. measured all: 3380001 |
Reflection shell | Resolution: 1.61→1.64 Å / % possible obs: 94.4 % / Redundancy: 36.5 % / Rmerge(I) obs: 4.232 / Num. measured all: 145095 / Num. unique obs: 3978 / CC1/2: 0.662 / Rpim(I) all: 0.698 / Rrim(I) all: 4.291 / Χ2: 1.03 / Net I/σ(I) obs: 1.7 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.61→42.86 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 15.5524 Å / Origin y: 22.8493 Å / Origin z: 21.8618 Å
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Refinement TLS group | Selection details: all |