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Open data
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Basic information
Entry | Database: PDB / ID: 3upm | ||||||
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Title | Crystal Structure of PTE mutant H254Q/H257F/K185R/I274N | ||||||
![]() | Parathion hydrolase | ||||||
![]() | HYDROLASE / metalloenzyme / TIM barrel / nerve agents / phosphotriesterase | ||||||
Function / homology | ![]() aryldialkylphosphatase / aryldialkylphosphatase activity / catabolic process / zinc ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tsai, P. / Fox, N.G. / Li, Y. / Barondeau, D.P. / Raushel, F.M. | ||||||
![]() | ![]() Title: Enzymes for the homeland defense: optimizing phosphotriesterase for the hydrolysis of organophosphate nerve agents. Authors: Tsai, P.C. / Fox, N. / Bigley, A.N. / Harvey, S.P. / Barondeau, D.P. / Raushel, F.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 145.9 KB | Display | ![]() |
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PDB format | ![]() | 112.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.4 KB | Display | ![]() |
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Full document | ![]() | 439.6 KB | Display | |
Data in XML | ![]() | 28.3 KB | Display | |
Data in CIF | ![]() | 41.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ur2C ![]() 3ur5C ![]() 3uraC ![]() 3urbC ![]() 3urnC ![]() 3urqC ![]() 1hzyS 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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Unit cell |
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Components
#1: Protein | Mass: 35559.414 Da / Num. of mol.: 2 / Fragment: UNP residues 35-361 / Mutation: H254Q/H257F/K185R/I274N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CO / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.74 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2 uL 11.2 mg/mL protein + 2 uL well solution (0.1 M MES, pH 6.0, 18% PEG5000 MME) over 500 uL well solution, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 26, 2009 |
Radiation | Monochromator: Si(111), side scattering I-beam bent single crystal, asymmetric cut 4.9650 deg Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. all: 47614 / Num. obs: 47545 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Biso Wilson estimate: 31.7 Å2 / Rsym value: 0.116 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 8.8 % / Mean I/σ(I) obs: 6.8 / Num. unique all: 4692 / Rsym value: 0.355 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1HZY Resolution: 1.95→50 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 17.6581 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.97 Å2 / Biso mean: 38.3136 Å2 / Biso min: 19.88 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.02 Å
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Xplor file |
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