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Open data
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Basic information
Entry | Database: PDB / ID: 7buk | ||||||
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Title | T1 lipase mutant - 5M (D43E/T118N/E226D/E250L/N304E) | ||||||
![]() | Lipase | ||||||
![]() | HYDROLASE / lipase / mutation / triglycerides | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ishak, S.N.H. / Rahman, R.N.Z.R.A. / Ali, M.S.M. / Leow, A.T.C. / Kamarudin, N.H.A. | ||||||
![]() | ![]() Title: Structure elucidation and docking analysis of 5M mutant of T1 lipase Geobacillus zalihae. Authors: Ishak, S.N.H. / Kamarudin, N.H.A. / Ali, M.S.M. / Leow, A.T.C. / Shariff, F.M. / Rahman, R.N.Z.R.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 166.3 KB | Display | ![]() |
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PDB format | ![]() | 129.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.6 KB | Display | ![]() |
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Full document | ![]() | 449.8 KB | Display | |
Data in XML | ![]() | 29.7 KB | Display | |
Data in CIF | ![]() | 41.8 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 |
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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
#1: Protein | Mass: 45413.684 Da / Num. of mol.: 2 / Mutation: D43E/T118N/E226D/E250L/N304E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | Sequence details | This is D43E/T118N/E226D/E250L/N304E mutant. And 18 N-terminal residues (MSPISRHHHHHHLVPRGS) are ...This is D43E/T118N/E226D/E250L/N304E mutant. And 18 N-terminal residues (MSPISRHHHH | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.91 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.5 M sodium cacodylate trihydrate, 0.4 M sodium citrate tribasic pH 6.5, 0.2 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: CCD / Date: Jun 19, 2019 / Details: DEXTRIS 200K |
Radiation | Monochromator: cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→40 Å / Num. obs: 24822 / % possible obs: 90.9 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.65→2.7 Å / Rmerge(I) obs: 0.129 / Num. unique obs: 38251 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2DSN Resolution: 2.644→35.1 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.856 / SU B: 11.524 / SU ML: 0.241 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.376 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.42 Å2 / Biso mean: 15.927 Å2 / Biso min: 0.5 Å2
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Refinement step | Cycle: final / Resolution: 2.644→35.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.644→2.712 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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