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Yorodumi- PDB-6eqf: Crystal structure of a polyethylene terephthalate degrading hydro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6eqf | |||||||||
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Title | Crystal structure of a polyethylene terephthalate degrading hydrolase from Ideonella sakaiensis in spacegroup P212121 | |||||||||
Components | Poly(ethylene terephthalate) hydrolase | |||||||||
Keywords | HYDROLASE / PETase / PET degradation / a/b hydrolase | |||||||||
Function / homology | Function and homology information poly(ethylene terephthalate) hydrolase / acetylesterase activity / carboxylic ester hydrolase activity / cellular response to organic substance / xenobiotic catabolic process / extracellular region Similarity search - Function | |||||||||
Biological species | Ideonella sakaiensis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||
Authors | Austin, H.P. / Allen, M.D. / Johnson, C.W. / Beckham, G.T. / McGeehan, J.E. | |||||||||
Funding support | United States, United Kingdom, 2items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 Title: Characterization and engineering of a plastic-degrading aromatic polyesterase. Authors: Austin, H.P. / Allen, M.D. / Donohoe, B.S. / Rorrer, N.A. / Kearns, F.L. / Silveira, R.L. / Pollard, B.C. / Dominick, G. / Duman, R. / El Omari, K. / Mykhaylyk, V. / Wagner, A. / Michener, W. ...Authors: Austin, H.P. / Allen, M.D. / Donohoe, B.S. / Rorrer, N.A. / Kearns, F.L. / Silveira, R.L. / Pollard, B.C. / Dominick, G. / Duman, R. / El Omari, K. / Mykhaylyk, V. / Wagner, A. / Michener, W.E. / Amore, A. / Skaf, M.S. / Crowley, M.F. / Thorne, A.W. / Johnson, C.W. / Woodcock, H.L. / McGeehan, J.E. / Beckham, G.T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6eqf.cif.gz | 73 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6eqf.ent.gz | 51.6 KB | Display | PDB format |
PDBx/mmJSON format | 6eqf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eq/6eqf ftp://data.pdbj.org/pub/pdb/validation_reports/eq/6eqf | HTTPS FTP |
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-Related structure data
Related structure data | 6eqdSC 6eqeC 6eqgC 6eqhC 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: 31341.924 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ideonella sakaiensis (bacteria) / Gene: ISF6_4831 / Production host: Escherichia coli (E. coli) / Strain (production host): C41 References: UniProt: A0A0K8P6T7, poly(ethylene terephthalate) hydrolase |
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#2: Chemical | ChemComp-CL / |
#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: 1.81 Å3/Da / Density % sol: 32.1 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 NH4Cl, 0.1 M MES, pH 6.0 20% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 10, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→68.24 Å / Num. obs: 25470 / % possible obs: 98.8 % / Redundancy: 5.7 % / CC1/2: 0.991 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.049 / Rrim(I) all: 0.118 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 3652 / CC1/2: 0.905 / Rpim(I) all: 0.147 / Rrim(I) all: 0.356 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6EQD Resolution: 1.7→46.732 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.37 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→46.732 Å
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Refine LS restraints |
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LS refinement shell |
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