+Open data
-Basic information
Entry | Database: PDB / ID: 6jtu | ||||||
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Title | Crystal structure of MHETase from Ideonella sakaiensis | ||||||
Components | Mono(2-hydroxyethyl) terephthalate hydrolase | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information mono(ethylene terephthalate) hydrolase / carboxylic ester hydrolase activity / cellular response to organic substance / xenobiotic catabolic process / cell outer membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Ideonella sakaiensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Sagong, H.-Y. / Seo, H. / Kim, K.-J. | ||||||
Citation | Journal: Acs Catalysis / Year: 2020 Title: Decomposition of PET film by MHETase using Exo-PETase function Authors: Sagong, H.-Y. / Seo, H. / Kim, T. / Son, H. / Joo, S. / Lee, S. / Kim, S. / Woo, J.-S. / Hwang, S. / Kim, K.-J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jtu.cif.gz | 329.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jtu.ent.gz | 273.9 KB | Display | PDB format |
PDBx/mmJSON format | 6jtu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jt/6jtu ftp://data.pdbj.org/pub/pdb/validation_reports/jt/6jtu | HTTPS FTP |
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-Related 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
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 64178.004 Da / Num. of mol.: 3 / Fragment: feruloyl esterase domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ideonella sakaiensis (bacteria) / Strain: 201-F6 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: A0A0K8P8E7, mono(ethylene terephthalate) hydrolase |
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-Non-polymers , 6 types, 737 molecules
#2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Chemical | ChemComp-FMT / | #6: Chemical | #7: 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: 4.49 Å3/Da / Density % sol: 72.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG3350, HEPES, Tacsimate pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 18, 2018 |
Radiation | Monochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 196929 / % possible obs: 97.7 % / Redundancy: 3.5 % / CC1/2: 0.977 / Rpim(I) all: 0.063 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 2.1→2.14 Å / Num. unique obs: 9385 / CC1/2: 0.861 / Rpim(I) all: 0.175 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→33.21 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.393 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.115 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: 105.53 Å2 / Biso mean: 29.49 Å2 / Biso min: 19.12 Å2
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Refinement step | Cycle: final / Resolution: 2.1→33.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.102→2.156 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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