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Yorodumi- PDB-7w1l: Crystal structure of carboxylesterase mutant from Thermobifida fu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7w1l | ||||||
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Title | Crystal structure of carboxylesterase mutant from Thermobifida fusca with C8X | ||||||
Components | Carboxylesterase | ||||||
Keywords | HYDROLASE / plastic degradation / catalysis | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermobifida fusca (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å | ||||||
Authors | Han, X. / Gerlis, H. / Li, Z. / Gao, J. / Wei, R. / Liu, W. | ||||||
Funding support | 1items
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Citation | Journal: Acs Catalysis / Year: 2022 Title: Structural Insights into (Tere)phthalate-Ester Hydrolysis by a Carboxylesterase and Its Role in Promoting PET Depolymerization Authors: Von Haugwitz, G. / Han, X. / Pfaff, L. / Li, Q. / Wei, H. / Gao, J. / Methling, K. / Ao, Y. / Brack, Y. / Mican, J. / Feiler, C.G. / Weiss, M.S. / Bednar, D. / Palm, G.J. / Lalk, M. / ...Authors: Von Haugwitz, G. / Han, X. / Pfaff, L. / Li, Q. / Wei, H. / Gao, J. / Methling, K. / Ao, Y. / Brack, Y. / Mican, J. / Feiler, C.G. / Weiss, M.S. / Bednar, D. / Palm, G.J. / Lalk, M. / Lammers, M. / Damborsky, J. / Weber, G. / Liu, W. / Bornscheuer, U.T. / Wei, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7w1l.cif.gz | 112.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7w1l.ent.gz | 82.4 KB | Display | PDB format |
PDBx/mmJSON format | 7w1l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w1/7w1l ftp://data.pdbj.org/pub/pdb/validation_reports/w1/7w1l | HTTPS FTP |
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-Related structure data
Related structure data | 7w1iC 7w1jC 7w1kC 2ogtS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 52970.543 Da / Num. of mol.: 1 / Mutation: E319L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermobifida fusca (bacteria) / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P86325, carboxylesterase |
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#2: Chemical | ChemComp-C8X / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.59 % / Mosaicity: 1.559 ° |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 1.0 M sodium citrate, 0.1 M Imidazole pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.43→25 Å / Num. obs: 18029 / % possible obs: 99.7 % / Redundancy: 7.2 % / Biso Wilson estimate: 26.05 Å2 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.072 / Rrim(I) all: 0.195 / Χ2: 0.885 / Net I/σ(I): 4 / Num. measured all: 130648 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OGT Resolution: 2.44→25 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 21.85 / 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 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.06 Å2 / Biso mean: 28.1606 Å2 / Biso min: 11.62 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.44→25 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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