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Yorodumi- PDB-5tif: x-ray structure of acyl-CoA thioesterase I, TesA, triple mutant M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tif | ||||||
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Title | x-ray structure of acyl-CoA thioesterase I, TesA, triple mutant M141L/Y145K/L146K 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 / long-chain fatty acyl-CoA hydrolase activity / phosphatidyl phospholipase B activity / lysophospholipase / palmitoyl-CoA hydrolase / fatty acyl-[ACP] hydrolase activity / oleoyl-[acyl-carrier-protein] hydrolase / lysophospholipase activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / arylesterase activity ...arylesterase / long-chain fatty acyl-CoA hydrolase activity / phosphatidyl phospholipase B activity / lysophospholipase / palmitoyl-CoA hydrolase / fatty acyl-[ACP] hydrolase activity / oleoyl-[acyl-carrier-protein] hydrolase / 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 | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 0.97 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 | 5tif.cif.gz | 113 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tif.ent.gz | 85.7 KB | Display | PDB format |
PDBx/mmJSON format | 5tif.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5tif_validation.pdf.gz | 454.6 KB | Display | wwPDB validaton report |
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Full document | 5tif_full_validation.pdf.gz | 458.7 KB | Display | |
Data in XML | 5tif_validation.xml.gz | 15 KB | Display | |
Data in CIF | 5tif_validation.cif.gz | 23.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ti/5tif ftp://data.pdbj.org/pub/pdb/validation_reports/ti/5tif | HTTPS FTP |
-Related structure data
Related structure data | 5ticC 5tidSC 5tieC C: citing same article (ref.) S: Starting model for refinement |
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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: Chemical | ChemComp-PEG / |
#4: 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: 2.19 Å3/Da / Density % sol: 43.72 % |
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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 19, 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: 0.97→50 Å / Num. obs: 102836 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.06 / Rsym value: 0.006 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 0.97→1.07 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 2.4 / % possible all: 92.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5tid Resolution: 0.97→40.59 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.98 / SU B: 0.623 / SU ML: 0.014 / Cross valid method: THROUGHOUT / ESU R: 0.019 / ESU R Free: 0.019 / 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: 16.085 Å2
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Refinement step | Cycle: 1 / Resolution: 0.97→40.59 Å
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Refine LS restraints |
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