+Open data
-Basic information
Entry | Database: PDB / ID: 6qz4 | ||||||
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Title | Structure of MHETase from Ideonella sakaiensis | ||||||
Components | Mono(2-hydroxyethyl) terephthalate hydrolase | ||||||
Keywords | HYDROLASE / MHETase / PET degradation / STRUCTURAL GENOMICS / plastic-binding protein | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Allen, M.D. / Johnson, C.W. / Knott, B.C. / Beckham, G.T. / McGeehan, J.E. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: Characterization and engineering of a two-enzyme system for plastics depolymerization. Authors: Knott, B.C. / Erickson, E. / Allen, M.D. / Gado, J.E. / Graham, R. / Kearns, F.L. / Pardo, I. / Topuzlu, E. / Anderson, J.J. / Austin, H.P. / Dominick, G. / Johnson, C.W. / Rorrer, N.A. / ...Authors: Knott, B.C. / Erickson, E. / Allen, M.D. / Gado, J.E. / Graham, R. / Kearns, F.L. / Pardo, I. / Topuzlu, E. / Anderson, J.J. / Austin, H.P. / Dominick, G. / Johnson, C.W. / Rorrer, N.A. / Szostkiewicz, C.J. / Copie, V. / Payne, C.M. / Woodcock, H.L. / Donohoe, B.S. / Beckham, G.T. / McGeehan, J.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qz4.cif.gz | 255.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qz4.ent.gz | 200.2 KB | Display | PDB format |
PDBx/mmJSON format | 6qz4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qz4_validation.pdf.gz | 451.2 KB | Display | wwPDB validaton report |
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Full document | 6qz4_full_validation.pdf.gz | 459 KB | Display | |
Data in XML | 6qz4_validation.xml.gz | 54.4 KB | Display | |
Data in CIF | 6qz4_validation.cif.gz | 83.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qz/6qz4 ftp://data.pdbj.org/pub/pdb/validation_reports/qz/6qz4 | HTTPS FTP |
-Related structure data
Related structure data | 6qz1SC 6qz2C 6qz3C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 64221.742 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ideonella sakaiensis (bacteria) / Gene: ISF6_0224 / Plasmid: pCJ136 / Production host: Escherichia coli (E. coli) / Variant (production host): C41 References: UniProt: A0A0K8P8E7, mono(ethylene terephthalate) hydrolase #2: Chemical | #3: Chemical | #4: 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: 2.61 Å3/Da / Density % sol: 52.82 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: ammonium acetate (pH 4.5), 22.5% PEG 10000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 22, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→46.24 Å / Num. obs: 122377 / % possible obs: 98.2 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.028 / Rrim(I) all: 0.073 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 17402 / CC1/2: 0.914 / Rpim(I) all: 0.231 / Rrim(I) all: 0.598 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6QZ1 Resolution: 1.8→46.239 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.2 / Phase error: 23.44
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→46.239 Å
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Refine LS restraints |
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LS refinement shell |
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