+Open data
-Basic information
Entry | Database: PDB / ID: 6ane | |||||||||
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Title | Crystal Structure of Ideonella sakaiensis PET Hydrolase | |||||||||
Components | Poly(ethylene terephthalate) hydrolase | |||||||||
Keywords | HYDROLASE / PETase / AB hydrolase / cutinase / plastic | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.02 Å | |||||||||
Authors | Galaz-Davison, P. / Sotomayor, M. / Parra, L.P. / Ramirez-Sarmiento, C.A. | |||||||||
Funding support | United States, Chile, 2items
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Citation | Journal: Biophys. J. / Year: 2018 Title: Active Site Flexibility as a Hallmark for Efficient PET Degradation by I. sakaiensis PETase. Authors: Fecker, T. / Galaz-Davison, P. / Engelberger, F. / Narui, Y. / Sotomayor, M. / Parra, L.P. / Ramirez-Sarmiento, C.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ane.cif.gz | 164.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ane.ent.gz | 127.7 KB | Display | PDB format |
PDBx/mmJSON format | 6ane.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/an/6ane ftp://data.pdbj.org/pub/pdb/validation_reports/an/6ane | HTTPS FTP |
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-Related structure data
Related structure data | 4cg1S 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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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 28782.916 Da / Num. of mol.: 3 / Fragment: residues 28-290 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ideonella sakaiensis (strain 201-F6) (bacteria) Strain: 201-F6 / Gene: ISF6_4831 / Plasmid: pET24b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: A0A0K8P6T7, poly(ethylene terephthalate) hydrolase #2: Chemical | ChemComp-MG / | #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: 2.96 Å3/Da / Density % sol: 58.41 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES pH 6.5 1.6 M MgSO4 20% Glycerol |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54187 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Aug 5, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54187 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→116.93 Å / Num. obs: 67721 / % possible obs: 95.9 % / Redundancy: 6 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 9.83 |
Reflection shell | Resolution: 2.02→2.05 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 2 / Num. unique obs: 3054 / % possible all: 92.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4cg1 Resolution: 2.02→116.93 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.865 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.144 / 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: 21.221 Å2
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Refinement step | Cycle: 1 / Resolution: 2.02→116.93 Å
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Refine LS restraints |
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