+Open data
-Basic information
Entry | Database: PDB / ID: 8ve9 | ||||||
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Title | IsPETase - ACCCETN mutant - CombiPETase | ||||||
Components | Poly(ethylene terephthalate) hydrolase | ||||||
Keywords | HYDROLASE / PETase / protein engineering | ||||||
Function / homology | Function and homology information poly(ethylene terephthalate) hydrolase / acetylesterase activity / : / carboxylic ester hydrolase activity / xenobiotic catabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Piscinibacter sakaiensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Joho, Y. / Royan, S. / Newton, S. / Caputo, A.T. / Ardevol Grau, A. / Jackson, C. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Chembiochem / Year: 2024 Title: Enhancing PET Degrading Enzymes: A Combinatory Approach. Authors: Joho, Y. / Royan, S. / Caputo, A.T. / Newton, S. / Peat, T.S. / Newman, J. / Jackson, C. / Ardevol, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ve9.cif.gz | 115.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ve9.ent.gz | 85.1 KB | Display | PDB format |
PDBx/mmJSON format | 8ve9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ve9_validation.pdf.gz | 435.1 KB | Display | wwPDB validaton report |
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Full document | 8ve9_full_validation.pdf.gz | 435.9 KB | Display | |
Data in XML | 8ve9_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 8ve9_validation.cif.gz | 19.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ve/8ve9 ftp://data.pdbj.org/pub/pdb/validation_reports/ve/8ve9 | HTTPS FTP |
-Related structure data
Related structure data | 8vekC 8velC 8vemC 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: 28647.842 Da / Num. of mol.: 1 / Mutation: K95N, S136E, A179C, D186A, S214T, N233C, S282C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Piscinibacter sakaiensis (bacteria) / Gene: ISF6_4831 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A0K8P6T7, poly(ethylene terephthalate) hydrolase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-CL / | #4: 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: 2.36 Å3/Da / Density % sol: 47.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.71 Details: 22.4% (w/v) PEG 3350, 0.23 M TMAO, 0.1 M trisodium citrate-citric acid pH 3.71 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 18, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→51.588 Å / Num. obs: 36462 / % possible obs: 99.8 % / Redundancy: 13.5 % / CC1/2: 0.999 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.6→1.6 Å / Num. unique obs: 1794 / CC1/2: 0.972 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→51.588 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.968 / WRfactor Rfree: 0.161 / WRfactor Rwork: 0.139 / SU B: 1.507 / SU ML: 0.05 / Average fsc free: 0.975 / Average fsc work: 0.9814 / Cross valid method: FREE R-VALUE / ESU R: 0.068 / ESU R Free: 0.07 Details: Hydrogens have been added in their 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 / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.262 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→51.588 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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