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Yorodumi- PDB-5tid: X-ray structure of acyl-CoA thioesterase I, TesA, mutant M141L/Y1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tid | ||||||
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Title | X-ray structure of acyl-CoA thioesterase I, TesA, mutant M141L/Y145K/L146K at pH 5 in complex with octanoic acid | ||||||
Components | Acyl-CoA thioesterase I | ||||||
Keywords | HYDROLASE / Thioesterase / TesA / fatty acid / octanoic acid | ||||||
Function / homology | Function and homology information arylesterase / phosphatidyl phospholipase B activity / lysophospholipase / : / palmitoyl-CoA hydrolase / : / : / fatty acyl-CoA hydrolase activity / oleoyl-[acyl-carrier-protein] hydrolase / lysophospholipase activity ...arylesterase / phosphatidyl phospholipase B activity / lysophospholipase / : / palmitoyl-CoA hydrolase / : / : / fatty acyl-CoA hydrolase activity / oleoyl-[acyl-carrier-protein] hydrolase / lysophospholipase activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / arylesterase activity / lipid metabolic process / outer membrane-bounded periplasmic space / peptidase activity / proteolysis / identical protein binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | 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 | United States, 1items
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Citation | Journal: ACS Catal / Year: 2017 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tid.cif.gz | 60.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tid.ent.gz | 41.7 KB | Display | PDB format |
PDBx/mmJSON format | 5tid.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ti/5tid ftp://data.pdbj.org/pub/pdb/validation_reports/ti/5tid | HTTPS FTP |
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-Related structure data
Related structure data | 5ticSC 5tieC 5tifC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-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.) Escherichia coli (E. coli) / Gene: tesA, apeA, pldC, b0494, JW0483 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) References: UniProt: P0ADA1, Hydrolases; Acting on ester bonds; Thioester hydrolases, lysophospholipase |
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#2: Chemical | ChemComp-OCA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.56 % |
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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 |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
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 |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
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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 mean: 11.811 Å2
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Refinement step | Cycle: 1 / Resolution: 1.2→40.85 Å
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Refine LS restraints |
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