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Yorodumi- PDB-6ths: High resolution crystal structure of Leaf-branch cutinase S165A v... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ths | ||||||
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Title | High resolution crystal structure of Leaf-branch cutinase S165A 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: 1.1 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 | 6ths.cif.gz | 125.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ths.ent.gz | 95.3 KB | Display | PDB format |
PDBx/mmJSON format | 6ths.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/th/6ths ftp://data.pdbj.org/pub/pdb/validation_reports/th/6ths | HTTPS FTP |
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-Related structure data
Related structure data | 6thtC 4eb0S 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: 27783.992 Da / Num. of mol.: 1 / Mutation: S165A 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-DIO / |
#3: 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: 44.15 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion / pH: 9 / Details: 0.1 M Bicine pH 9.0, 2% Dioxane, 12% PEG 20000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97907 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 2, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97907 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.1→47.51 Å / Num. obs: 98700 / % possible obs: 99.6 % / Redundancy: 12.711 % / Biso Wilson estimate: 15.012 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.07 / Χ2: 1.152 / Net I/σ(I): 18.06 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-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: 1.1→47.51 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.978 / SU B: 2.066 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.03 / ESU R Free: 0.032 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: 70.19 Å2 / Biso mean: 15.091 Å2 / Biso min: 9 Å2
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Refinement step | Cycle: final / Resolution: 1.1→47.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.1→1.127 Å / Rfactor Rfree error: 0
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