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- PDB-3a3w: Structure of OpdA mutant (G60A/A80V/S92A/R118Q/K185R/Q206P/D208G/... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3a3w | ||||||
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Title | Structure of OpdA mutant (G60A/A80V/S92A/R118Q/K185R/Q206P/D208G/I260T/G273S) with diethyl 4-methoxyphenyl phosphate bound in the active site | ||||||
![]() | 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. / Tawfik, D.S. / Schenk, G. / Jackson, C.J. / Foo, J.L. / Tokuriki, N. / Afriat, L. / Carr, P.D. / Kim, H.K. | ||||||
![]() | ![]() Title: Conformational sampling, catalysis, and evolution of the bacterial phosphotriesterase Authors: Jackson, C.J. / Foo, J.-L. / Tokuriki, N. / Afriat, L. / Carr, P.D. / Kim, H.-K. / Schenk, G. / Tawfik, D.S. / 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 | ![]() | 86.1 KB | Display | ![]() |
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PDB format | ![]() | 62.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 775.8 KB | Display | ![]() |
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Full document | ![]() | 781 KB | Display | |
Data in XML | ![]() | 17.6 KB | Display | |
Data in CIF | ![]() | 26.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3a3xC ![]() 3a4jC ![]() 2d2jS C: citing same article ( S: Starting model for refinement |
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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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Unit cell |
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Components
#1: Protein | Mass: 35643.582 Da / Num. of mol.: 1 / Fragment: UNP residues 32-360 Mutation: G60A, A80V, S92A, R118Q, K185R, Q206P, D208G, I260T, G273S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | ChemComp-EPL / | #4: 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: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 13, 2007 Details: flat collimating mirror, double crystal monochromator, toroid focusing mirror |
Radiation | Monochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→40 Å / Num. all: 43843 / Num. obs: 43843 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.7→1.76 Å / % possible all: 51.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2D2J Resolution: 1.85→29.8 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.976 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.112 / 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: 25 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→29.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
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