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- PDB-4j5n: Crystal Structure of a Deinococcus radiodurans PTE-like lactonase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4j5n | ||||||
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Title | Crystal Structure of a Deinococcus radiodurans PTE-like lactonase (drPLL) mutant Y28L/D71N/E101G/E179D/V235L/L270M | ||||||
![]() | Phosphotriesterase, putative | ||||||
![]() | HYDROLASE / Metalloenzyme / Tim Barrel / Nerve agent / Phosphotriesterase / Lactonase | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Meier, M.M. / Rajendran, C. / Malisi, C. / Fox, N.G. / Xu, C. / Schlee, S. / Barondeau, D.P. / Hocker, B. / Sterner, R. / Raushel, F.M. | ||||||
![]() | ![]() Title: Molecular engineering of organophosphate hydrolysis activity from a weak promiscuous lactonase template. Authors: Meier, M.M. / Rajendran, C. / Malisi, C. / Fox, N.G. / Xu, C. / Schlee, S. / Barondeau, D.P. / Hocker, B. / Sterner, R. / 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 | ![]() | 80.2 KB | Display | ![]() |
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PDB format | ![]() | 58 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430.1 KB | Display | ![]() |
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Full document | ![]() | 431 KB | Display | |
Data in XML | ![]() | 15.3 KB | Display | |
Data in CIF | ![]() | 22.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4j2mC ![]() 4j35C ![]() 3fdkS 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
#1: Protein | Mass: 34704.102 Da / Num. of mol.: 1 / Mutation: Y28L, D71N, E101G, E179D, V235L, L270M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: Dr0930 (gi 15805954), DR_0930 / Production host: ![]() ![]() | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.22 Å3/Da / Density % sol: 61.8 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 2 uL of protein (~10 mg/mL) and 2 uL of well solution (0.1 M imidazole pH 8.0, 10% PEG 8000, 0.2 M Ca(OAc)2 ) were mixed and placed on a siliconized coverslip over 500 uL of the well ...Details: 2 uL of protein (~10 mg/mL) and 2 uL of well solution (0.1 M imidazole pH 8.0, 10% PEG 8000, 0.2 M Ca(OAc)2 ) were mixed and placed on a siliconized coverslip over 500 uL of the well solution. Cryo 14% EG, 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: Jul 23, 2010 |
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: 2.05→50 Å / Num. obs: 29424 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18.4 % / Biso Wilson estimate: 38.6 Å2 / Rsym value: 0.137 / Net I/σ(I): 36.5 |
Reflection shell | Resolution: 2.05→2.09 Å / Redundancy: 19.1 % / Mean I/σ(I) obs: 7.8 / Num. unique all: 1417 / Rsym value: 0.473 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3FDK Resolution: 2.05→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.05→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.07 Å /
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