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- PDB-3c86: OpdA from agrobacterium radiobacter with bound product diethyl th... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3c86 | |||||||||
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Title | OpdA from agrobacterium radiobacter with bound product diethyl thiophosphate from crystal soaking with tetraethyl dithiopyrophosphate- 1.8 A | |||||||||
![]() | Phosphotriesterase | |||||||||
![]() | HYDROLASE / phosphotriesterase / opdA / metalloenzyme | |||||||||
Function / homology | ![]() catabolic process / hydrolase activity, acting on ester bonds / zinc ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Ollis, D.L. / Jackson, C.J. / Foo, J.L. / Kim, H.K. / Carr, P.D. / Liu, J.W. / Salem, G. | |||||||||
![]() | ![]() Title: In crystallo capture of a Michaelis complex and product-binding modes of a bacterial phosphotriesterase Authors: Jackson, C.J. / Foo, J.L. / Kim, H.K. / Carr, P.D. / Liu, J.W. / Salem, G. / Ollis, D.L. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 86 KB | Display | ![]() |
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PDB format | ![]() | 62.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.5 KB | Display | ![]() |
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Full document | ![]() | 449 KB | Display | |
Data in XML | ![]() | 17.1 KB | Display | |
Data in CIF | ![]() | 25.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2r1kC ![]() 2r1lC ![]() 2r1mC ![]() 2r1nC ![]() 2r1pC ![]() 2d2jS 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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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 35572.527 Da / Num. of mol.: 1 / Fragment: UNP residues 33-360 / Mutation: S92A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 291 molecules ![](data/chem/img/FE2.gif)
![](data/chem/img/CO.gif)
![](data/chem/img/DPJ.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CO.gif)
![](data/chem/img/DPJ.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FE2 / |
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#3: Chemical | ChemComp-CO / |
#4: Chemical | ChemComp-DPJ / |
#5: Chemical | ChemComp-EDO / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.23 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG3350, 0.2M NaNO3, pH7, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 24, 2006 / Details: Confocal Mirrors |
Radiation | Monochromator: OSMIC CONFOCAL OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 39491 / Num. obs: 39491 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.8→1.91 Å / % possible all: 93.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2D2J Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.921 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 24.42 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
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