[English] 日本語
![](img/lk-miru.gif)
- PDB-5tid: X-ray structure of acyl-CoA thioesterase I, TesA, mutant M141L/Y1... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5tid | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray structure of acyl-CoA thioesterase I, TesA, mutant M141L/Y145K/L146K at pH 5 in complex with octanoic acid | ||||||
![]() | Acyl-CoA thioesterase I | ||||||
![]() | HYDROLASE / Thioesterase / TesA / fatty acid / octanoic acid | ||||||
Function / homology | ![]() arylesterase / phosphatidyl phospholipase B activity / lysophospholipase / palmitoyl-CoA hydrolase / fatty acyl-[ACP] hydrolase activity / oleoyl-[acyl-carrier-protein] hydrolase / fatty acyl-CoA hydrolase activity / lysophospholipase activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / arylesterase activity ...arylesterase / phosphatidyl phospholipase B activity / lysophospholipase / palmitoyl-CoA hydrolase / fatty acyl-[ACP] hydrolase activity / oleoyl-[acyl-carrier-protein] hydrolase / fatty acyl-CoA hydrolase activity / lysophospholipase activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / arylesterase activity / lipid metabolic process / peptidase activity / outer membrane-bounded periplasmic space / proteolysis / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Thoden, J.B. / Holden, H.M. / Grisewood, M.J. / Hernandez Lozada, N.J. / Gifford, N.P. / Mendez-Perez, D. / Schoenberger, H.A. / Allan, M.F. / Pfleger, B.F. / Marines, C.D. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Computational Redesign of Acyl-ACP Thioesterase with Improved Selectivity toward Medium-Chain-Length Fatty Acids. Authors: Grisewood, M.J. / Hernandez Lozada, N.J. / Thoden, J.B. / Gifford, N.P. / Mendez-Perez, D. / Schoenberger, H.A. / Allan, M.F. / Floy, M.E. / Lai, R.Y. / Holden, H.M. / Pfleger, B.F. / Maranas, C.D. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 60.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 41.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 445.6 KB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 20 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ticSC ![]() 5tieC ![]() 5tifC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 20685.525 Da / Num. of mol.: 1 / Fragment: UNP residues 28-208 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P0ADA1, Hydrolases; Acting on ester bonds; Thioester hydrolases, lysophospholipase |
---|---|
#2: Chemical | ChemComp-OCA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.56 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 20-25% PEG-5000, 100 mM homopipes, 3 mM octanoic acid |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Jul 16, 2016 / Details: montel |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→50 Å / Num. obs: 56148 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.2→1.3 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 3 / % possible all: 97.3 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5TIC Resolution: 1.2→40.85 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 0.58 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.04 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.811 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.2→40.85 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|