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Yorodumi- PDB-6tht: High resolution crystal structure of a Leaf-branch compost cutina... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tht | ||||||
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Title | High resolution crystal structure of a Leaf-branch compost cutinase quintuple variant | ||||||
Components | LCC | ||||||
Keywords | HYDROLASE / SERINE ESTERASE / CUTINASE | ||||||
Function / homology | Function and homology information poly(ethylene terephthalate) hydrolase / acetylesterase activity / cutinase activity / cutinase / extracellular region Similarity search - Function | ||||||
Biological species | uncultured bacterium (environmental samples) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.14 Å | ||||||
Authors | Nomme, J. | ||||||
Citation | Journal: Nature / Year: 2020 Title: An engineered PET depolymerase to break down and recycle plastic bottles. Authors: Tournier, V. / Topham, C.M. / Gilles, A. / David, B. / Folgoas, C. / Moya-Leclair, E. / Kamionka, E. / Desrousseaux, M.L. / Texier, H. / Gavalda, S. / Cot, M. / Guemard, E. / Dalibey, M. / ...Authors: Tournier, V. / Topham, C.M. / Gilles, A. / David, B. / Folgoas, C. / Moya-Leclair, E. / Kamionka, E. / Desrousseaux, M.L. / Texier, H. / Gavalda, S. / Cot, M. / Guemard, E. / Dalibey, M. / Nomme, J. / Cioci, G. / Barbe, S. / Chateau, M. / Andre, I. / Duquesne, S. / Marty, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tht.cif.gz | 126.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tht.ent.gz | 96.3 KB | Display | PDB format |
PDBx/mmJSON format | 6tht.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/th/6tht ftp://data.pdbj.org/pub/pdb/validation_reports/th/6tht | HTTPS FTP |
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-Related structure data
Related structure data | 6thsC 4eb0S 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: 27647.975 Da / Num. of mol.: 1 / Mutation: Y127G/S165A/D238C/F243I/S283C Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured bacterium (environmental samples) Plasmid: pET26b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G9BY57, cutinase |
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#2: Chemical | ChemComp-IMD / |
#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-CIT / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.06 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion / pH: 8 / Details: 0.1 M Imidazole, 1 M Sodium Citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 19, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.14→94.75 Å / Num. obs: 87457 / % possible obs: 100 % / Redundancy: 9.5 % / Rrim(I) all: 0.102 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.14→1.16 Å / Redundancy: 9.2 % / Rmerge(I) obs: 1.051 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4356 / CC1/2: 0.744 / Rpim(I) all: 0.364 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4EB0 Resolution: 1.14→94.75 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.981 / SU B: 0.877 / SU ML: 0.018 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.025 / ESU R Free: 0.026 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 403.66 Å2 / Biso mean: 15.815 Å2 / Biso min: 7.64 Å2
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Refinement step | Cycle: final / Resolution: 1.14→94.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.143→1.172 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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