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- PDB-5z7j: Crystal structure of a lactonase double mutant in complex with li... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5z7j | ||||||
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Title | Crystal structure of a lactonase double mutant in complex with ligand l | ||||||
![]() | Lactonase for protein | ||||||
![]() | HYDROLASE / ALPHA/BETA-HYDROLASE / LACTONASE / ZEARALENONE | ||||||
Function / homology | glycerolipid catabolic process / triacylglycerol lipase activity / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / Chem-36J / 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 | ![]() | 450.6 KB | Display | ![]() |
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PDB format | ![]() | 368.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.9 MB | Display | ![]() |
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Full document | ![]() | 3 MB | Display | |
Data in XML | ![]() | 98 KB | Display | |
Data in CIF | ![]() | 137.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xo6C ![]() 5xo7C ![]() 5xo8C ![]() 5z5jC ![]() 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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1 | ![]()
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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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: Z518_04590 / Plasmid: pET-46 EK/LIC / Production host: ![]() ![]() #2: Chemical | ChemComp-36J / ( #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.94 % / Mosaicity: 0.908 ° |
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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 MX-300 / 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: 1.98→25 Å / Num. obs: 188099 / % possible obs: 97.7 % / Redundancy: 4 % / Biso Wilson estimate: 30.94 Å2 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.042 / Rrim(I) all: 0.085 / Χ2: 0.705 / Net I/σ(I): 10.6 / Num. measured all: 752400 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5IE4 Resolution: 1.98→24.714 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 22.46
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 90.35 Å2 / Biso mean: 36.0956 Å2 / Biso min: 18.93 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.98→24.714 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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