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Yorodumi- PDB-5tic: X-ray structure of wild-type E. coli Acyl-CoA thioesterase I at pH 5 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tic | ||||||
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Title | X-ray structure of wild-type E. coli Acyl-CoA thioesterase I at pH 5 | ||||||
Components | Acyl-CoA thioesterase I | ||||||
Keywords | HYDROLASE / Thioesterase / TesA / Fatty Acid | ||||||
Function / homology | Function and homology information arylesterase / phosphatidyl phospholipase B activity / lysophospholipase / palmitoyl-CoA hydrolase / fatty acyl-[ACP] hydrolase activity / fatty acyl-CoA hydrolase activity / oleoyl-[acyl-carrier-protein] hydrolase / 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 / 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 / peptidase activity / outer membrane-bounded periplasmic space / proteolysis / identical protein binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 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 | 5tic.cif.gz | 92.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tic.ent.gz | 68.1 KB | Display | PDB format |
PDBx/mmJSON format | 5tic.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ti/5tic ftp://data.pdbj.org/pub/pdb/validation_reports/ti/5tic | HTTPS FTP |
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-Related structure data
Related structure data | 5tidC 5tieC 5tifC 1u8uS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 20721.535 Da / Num. of mol.: 2 / 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 #2: Chemical | ChemComp-CL / | #3: Water | ChemComp-HOH / | |
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-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: 22-26% PEG-5000, 100 mM homopipesa |
-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 4, 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: 1.65→50 Å / Num. obs: 42019 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.65→1.75 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 1.9 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1u8u Resolution: 1.65→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.605 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.106 / 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: 20.632 Å2
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Refinement step | Cycle: 1 / Resolution: 1.65→50 Å
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Refine LS restraints |
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