+Open data
-Basic information
Entry | Database: PDB / ID: 6jtt | ||||||
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Title | MHETase in complex with BHET | ||||||
Components | Mono(2-hydroxyethyl) terephthalate hydrolase | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information mono(ethylene terephthalate) hydrolase / carboxylic ester hydrolase activity / : / xenobiotic catabolic process / cell outer membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Ideonella sakaiensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.51 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 | 6jtt.cif.gz | 321.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jtt.ent.gz | 268 KB | Display | PDB format |
PDBx/mmJSON format | 6jtt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jtt_validation.pdf.gz | 717.1 KB | Display | wwPDB validaton report |
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Full document | 6jtt_full_validation.pdf.gz | 735.6 KB | Display | |
Data in XML | 6jtt_validation.xml.gz | 62.9 KB | Display | |
Data in CIF | 6jtt_validation.cif.gz | 88.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jt/6jtt ftp://data.pdbj.org/pub/pdb/validation_reports/jt/6jtt | HTTPS FTP |
-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
#1: Protein | Mass: 65249.172 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 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-C8X / | #5: Water | ChemComp-HOH / | Nonpolymer details | C9C has a betahydroxy-covalent intermediate state with Serine225. | |
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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: 4.44 Å3/Da / Density % sol: 72.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / 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: Mar 12, 2019 |
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: 2.5→33.21 Å / Num. obs: 114235 / % possible obs: 98.2 % / Redundancy: 2.1 % / CC1/2: 0.982 / Rmerge(I) obs: 0.086 / Net I/σ(I): 15.75 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.308 / Num. unique obs: 5710 / CC1/2: 0.867 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.51→33.21 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.905 / SU B: 6.264 / SU ML: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.233 / ESU R Free: 0.201 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: 101.38 Å2 / Biso mean: 26.538 Å2 / Biso min: 9.33 Å2
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Refinement step | Cycle: final / Resolution: 2.51→33.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.507→2.572 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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