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Open data
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Basic information
Entry | Database: PDB / ID: 7ey3 | ||||||
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Title | Double cysteine mutations in T1 lipase | ||||||
![]() | Thermostable lipase | ||||||
![]() | HYDROLASE / disulphide bond / cysteine / lipase / site-directed mutagenesis / STRUCTURAL PROTEIN | ||||||
Function / homology | triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process / Alpha/Beta hydrolase fold / extracellular region / metal ion binding / triacylglycerol lipase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Hamdan, S.H. / Leow, T.C. / Yahaya, N.M. / Ali, M.S.M. / Jonet, M.A. / Mohamad Aris, S.N.A. / Maiangwa, J. | ||||||
![]() | ![]() Title: Knotting terminal ends of mutant T1 lipase with disulfide bond improved structure rigidity and stability. Authors: Hamdan, S.H. / Maiangwa, J. / Nezhad, N.G. / Ali, M.S.M. / Normi, Y.M. / Shariff, F.M. / Rahman, R.N.Z.R.A. / Leow, T.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 208.2 KB | Display | ![]() |
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PDB format | ![]() | 133.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.2 MB | Display | ![]() |
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Full document | ![]() | 3.2 MB | Display | |
Data in XML | ![]() | 30.1 KB | Display | |
Data in CIF | ![]() | 43.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2dsnS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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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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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 43237.191 Da / Num. of mol.: 2 / Mutation: S2C, A384C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 354 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.52 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.5M Sodium chloride, 0.1M Sodium citrate dihydrate pH 5.6, 2 % Ethylene imine polymer |
-Data collection
Diffraction | Mean temperature: 293.15 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: CCD / Date: Sep 17, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→40 Å / Num. obs: 59606 / % possible obs: 99.1 % / Redundancy: 3.2 % / Biso Wilson estimate: 18.39 Å2 / CC1/2: 0.861 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.04→2.08 Å / Num. unique obs: 107633 / CC1/2: 0.886 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2dsn Resolution: 2.04→33.46 Å / SU ML: 0.2283 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.3094 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.92 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.04→33.46 Å
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Refine LS restraints |
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LS refinement shell |
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