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Yorodumi- PDB-8j45: Crystal structure of a Pichia pastoris-expressed IsPETase variant -
+Open data
-Basic information
Entry | Database: PDB / ID: 8j45 | ||||||
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Title | Crystal structure of a Pichia pastoris-expressed IsPETase variant | ||||||
Components | Poly(ethylene terephthalate) hydrolase | ||||||
Keywords | HYDROLASE / PET hydrolase / alpha/beta hydrolase / Ideonella Sakaiensis | ||||||
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 | Ideonella sakaiensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.49 Å | ||||||
Authors | Li, X. / He, H.L. / Long, X. / Niu, D. / Huang, J.-W. / Chen, C.-C. / Guo, R.-T. | ||||||
Funding support | China, 1items
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Citation | Journal: Chem Eng J / Year: 2023 Title: Complete decomposition of poly(ethylene terephthalate) by crude PET hydrolytic enzyme produced in Pichia pastoris Authors: Chen, C.C. / Li, X. / Min, J. / Zeng, Z. / Ning, Z. / He, H. / Long, X. / Niu, D. / Peng, R. / Liu, X. / Yang, Y. / Huang, J.W. / Guo, R.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8j45.cif.gz | 73.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8j45.ent.gz | 51.4 KB | Display | PDB format |
PDBx/mmJSON format | 8j45.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j4/8j45 ftp://data.pdbj.org/pub/pdb/validation_reports/j4/8j45 | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27592.625 Da / Num. of mol.: 1 / Mutation: S121E,D186H,R224Q,N233K,R280A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ideonella sakaiensis (bacteria) / Gene: ISF6_4831 / Production host: Komagataella pastoris (fungus) References: UniProt: A0A0K8P6T7, poly(ethylene terephthalate) hydrolase | ||||
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#2: Sugar | ChemComp-NAG / #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: 2.01 Å3/Da / Density % sol: 38.68 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M Sodium chloride, 0.1M Sodium formate, 0.1M Bis-Tris propane pH 8.5, 25% v/v PEG Smear Medium |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34138 Å |
Detector | Type: Bruker PHOTON III / Detector: PIXEL / Date: Oct 4, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.34138 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→36.21 Å / Num. obs: 35713 / % possible obs: 96.3 % / Redundancy: 11 % / Rmerge(I) obs: 0.0428 / Net I/σ(I): 38.82 |
Reflection shell | Resolution: 1.49→1.51 Å / Rmerge(I) obs: 0.0888 / Mean I/σ(I) obs: 11.47 / Num. unique obs: 1443 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→36.21 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 0.884 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.813 Å2
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Refinement step | Cycle: 1 / Resolution: 1.49→36.21 Å
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Refine LS restraints |
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