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Yorodumi- PDB-7pzj: Structure of a bacteroidetal polyethylene terephthalate (PET) esterase -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pzj | |||||||||
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Title | Structure of a bacteroidetal polyethylene terephthalate (PET) esterase | |||||||||
Components | Lipase | |||||||||
Keywords | HYDROLASE / hydrolases / metagenome / metagenomic screening / PET degradation / Polyethylene terephthalate (PET) / Bacteroidetes / Flavobacteriaceae | |||||||||
Function / homology | Secretion system C-terminal sorting domain / Secretion system C-terminal sorting domain / Alpha/Beta hydrolase fold / : / Lipase Function and homology information | |||||||||
Biological species | Chryseobacterium jeonii (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Zang, H. / Dierkes, R. / Perez-Garcia, P. / Weigert, S. / Sternagel, S. / Hallam, S.J. / Applegate, V. / Schumacher, J. / Schott, T. / Pleiss, J. ...Zang, H. / Dierkes, R. / Perez-Garcia, P. / Weigert, S. / Sternagel, S. / Hallam, S.J. / Applegate, V. / Schumacher, J. / Schott, T. / Pleiss, J. / Almeida, A. / Hoecker, B. / Smits, S.H. / Schmitz, R.A. / Chow, J. / Streit, W.R. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Front Microbiol / Year: 2021 Title: The Bacteroidetes Aequorivita sp. and Kaistella jeonii Produce Promiscuous Esterases With PET-Hydrolyzing Activity. Authors: Zhang, H. / Perez-Garcia, P. / Dierkes, R.F. / Applegate, V. / Schumacher, J. / Chibani, C.M. / Sternagel, S. / Preuss, L. / Weigert, S. / Schmeisser, C. / Danso, D. / Pleiss, J. / Almeida, ...Authors: Zhang, H. / Perez-Garcia, P. / Dierkes, R.F. / Applegate, V. / Schumacher, J. / Chibani, C.M. / Sternagel, S. / Preuss, L. / Weigert, S. / Schmeisser, C. / Danso, D. / Pleiss, J. / Almeida, A. / Hocker, B. / Hallam, S.J. / Schmitz, R.A. / Smits, S.H.J. / Chow, J. / Streit, W.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pzj.cif.gz | 115.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pzj.ent.gz | 87 KB | Display | PDB format |
PDBx/mmJSON format | 7pzj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pz/7pzj ftp://data.pdbj.org/pub/pdb/validation_reports/pz/7pzj | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 38911.117 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chryseobacterium jeonii (bacteria) / Gene: OA86_11720 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0C1F4U8 | ||||
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#2: Chemical | ChemComp-K / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 285 K / Method: vapor diffusion / Details: 0.1 M sodium aetate pH 4.6 and 25% (w/v) PEG 4000 |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 19, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→38.8 Å / Num. obs: 15447 / % possible obs: 99.95 % / Redundancy: 17.3 % / CC1/2: 0.997 / Net I/σ(I): 13.95 |
Reflection shell | Resolution: 2.1→2.175 Å / Mean I/σ(I) obs: 5.38 / Num. unique obs: 1505 / CC1/2: 0.945 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: own model Resolution: 2.1→49.08 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.92 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 130.51 Å2 / Biso mean: 29.1476 Å2 / Biso min: 12.13 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→49.08 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %
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