+Open data
-Basic information
Entry | Database: PDB / ID: 3ur5 | ||||||
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Title | Crystal Structure of PTE mutant K185R/I274N | ||||||
Components | Parathion hydrolase | ||||||
Keywords | HYDROLASE / metalloenzyme / TIM barrel / nerve agents / phosphotriesterase | ||||||
Function / homology | Function and homology information aryldialkylphosphatase / aryldialkylphosphatase activity / catabolic process / zinc ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Brevundimonas diminuta (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Tsai, P. / Fox, N.G. / Li, Y. / Barondeau, D.P. / Raushel, F.M. | ||||||
Citation | Journal: Biochemistry / Year: 2012 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ur5.cif.gz | 151.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ur5.ent.gz | 116.5 KB | Display | PDB format |
PDBx/mmJSON format | 3ur5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ur/3ur5 ftp://data.pdbj.org/pub/pdb/validation_reports/ur/3ur5 | HTTPS FTP |
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-Related structure data
Related structure data | 3upmC 3ur2C 3uraC 3urbC 3urnC 3urqC 1hzyS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35560.406 Da / Num. of mol.: 2 / Fragment: UNP residues 35-361 / Mutation: K185R/I274N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brevundimonas diminuta (bacteria) / Gene: opd / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A434, aryldialkylphosphatase #2: Chemical | #3: Chemical | ChemComp-CO / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.91 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2 uL 11.5 mg/mL protein + 2 uL seeding solution (24% PEG5000 MME, 4% dioxane, 1.0 mM cobalt chloride, 100 mM diethylphosphate, 0.1 M HEPES, pH 7.5) over 500 uL precipitating agent (25% ...Details: 2 uL 11.5 mg/mL protein + 2 uL seeding solution (24% PEG5000 MME, 4% dioxane, 1.0 mM cobalt chloride, 100 mM diethylphosphate, 0.1 M HEPES, pH 7.5) over 500 uL precipitating agent (25% PEG5000 MME), VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 25, 2009 |
Radiation | Monochromator: Si(111), Side scattering bent cube-root I-beam single crystal, asymmetric cut 4.965 degs Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 86462 / Num. obs: 86431 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18.3 % / Biso Wilson estimate: 23.4 Å2 / Rsym value: 0.071 / Net I/σ(I): 38.2 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 13 % / Mean I/σ(I) obs: 8.8 / Num. unique all: 8508 / Rsym value: 0.372 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HZY Resolution: 1.6→50 Å / Occupancy max: 1 / Occupancy min: 0.65 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 24.9633 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 63.51 Å2 / Biso mean: 27.1378 Å2 / Biso min: 12.08 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.66 Å
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Xplor file |
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