+Open data
-Basic information
Entry | Database: PDB / ID: 8vel | ||||||
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Title | IsPETase - ACCCC mutant | ||||||
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: 1.624 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 | 8vel.cif.gz | 163.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vel.ent.gz | 130.1 KB | Display | PDB format |
PDBx/mmJSON format | 8vel.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8vel_validation.pdf.gz | 422.3 KB | Display | wwPDB validaton report |
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Full document | 8vel_full_validation.pdf.gz | 422.2 KB | Display | |
Data in XML | 8vel_validation.xml.gz | 14 KB | Display | |
Data in CIF | 8vel_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ve/8vel ftp://data.pdbj.org/pub/pdb/validation_reports/ve/8vel | HTTPS FTP |
-Related structure data
Related structure data | 8ve9C 8vekC 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: 28608.896 Da / Num. of mol.: 1 / Mutation: A179C, T198C, D186A, 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: Water | ChemComp-HOH / | Has ligand of interest | N | Has protein modification | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.138 M ammonium sulfate; 30 w/v polyethylene glycol 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95372 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Nov 27, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 1.624→51.738 Å / Num. obs: 29388 / % possible obs: 94.5 % / Redundancy: 13.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.043 / Rrim(I) all: 0.161 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.624→1.739 Å / Redundancy: 10.4 % / Rmerge(I) obs: 1.698 / Num. unique obs: 1469 / CC1/2: 0.513 / Rpim(I) all: 0.531 / Rrim(I) all: 1.784 / % possible all: 63.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.624→51.74 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.949 / SU R Cruickshank DPI: 0.133 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.115 / SU Rfree Blow DPI: 0.102 / SU Rfree Cruickshank DPI: 0.096
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Displacement parameters | Biso mean: 21.21 Å2
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Refine analyze | Luzzati coordinate error obs: 0.21 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.624→51.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.624→1.69 Å
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Refinement TLS params. | Origin x: -7.5457 Å / Origin y: 18.3454 Å / Origin z: -14.0631 Å
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Refinement TLS group |
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