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Open data
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Basic information
Entry | Database: PDB / ID: 5z5j | ||||||
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Title | Crystal structure of a lactonase double mutant | ||||||
![]() | Lactonase for protein | ||||||
![]() | HYDROLASE / ALPHA/BETA-HYDROLASE / LACTONASE / ZEARALENONE | ||||||
Function / homology | glycerolipid catabolic process / triglyceride lipase activity / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / DI(HYDROXYETHYL)ETHER / AB hydrolase-1 domain-containing protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Zheng, Y.Y. / Liu, W.D. / Chen, C.C. / Guo, R.T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structure of a Mycoestrogen-Detoxifying Lactonase from Rhinocladiella mackenziei: Molecular Insight into ZHD Substrate Selectivity Authors: Zheng, Y.Y. / Liu, W.T. / Chen, C.C. / Hu, X.Y. / Liu, W.D. / Ko, T.P. / Tang, X.K. / Wei, H.L. / Huang, J.W. / Guo, R.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 429.6 KB | Display | ![]() |
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PDB format | ![]() | 353.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 501.4 KB | Display | ![]() |
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Full document | ![]() | 536.7 KB | Display | |
Data in XML | ![]() | 88.1 KB | Display | |
Data in CIF | ![]() | 124.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xo6C ![]() 5xo7C ![]() 5xo8C ![]() 5z7jC ![]() 5z97C ![]() 5ie4S 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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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29154.854 Da / Num. of mol.: 8 / Fragment: UNP residues 3-266 / Mutation: S105A, Y160A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: Z518_04590 / Plasmid: pET-46 EK/LIC / Production host: ![]() ![]() #2: Chemical | ChemComp-PEG / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.07 % / Mosaicity: 1.672 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2M Ammonium Sulfate, 0.085M Sodium Cacodylate pH 6.5, 25-28%(w/v) Polyethylene Glycol 8000 and 15%(v/v) Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Aug 2, 2017 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.18→25 Å / Num. obs: 143209 / % possible obs: 96.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 2.18→2.26 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.482 / % possible all: 94.1 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5IE4 Resolution: 2.15→24.7 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 23.23
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.71 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→24.7 Å
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Refine LS restraints |
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LS refinement shell |
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