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Yorodumi- PDB-7dzv: Cyrstal structure of PETase E186A mutant from Rhizobacter gummiphilus -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dzv | ||||||
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Title | Cyrstal structure of PETase E186A mutant from Rhizobacter gummiphilus | ||||||
Components | DLH domain-containing protein | ||||||
Keywords | HYDROLASE / PET hydrolase | ||||||
Function / homology | Dienelactone hydrolase / Dienelactone hydrolase family / Alpha/Beta hydrolase fold / hydrolase activity / Lipase Function and homology information | ||||||
Biological species | Rhizobacter gummiphilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Sagong, H.-Y. / Kim, K.-J. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: J Hazard Mater / Year: 2021 Title: Implications for the PET decomposition mechanism through similarity and dissimilarity between PETases from Rhizobacter gummiphilus and Ideonella sakaiensis. Authors: Sagong, H.Y. / Son, H.F. / Seo, H. / Hong, H. / Lee, D. / 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 | 7dzv.cif.gz | 73.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dzv.ent.gz | 50.8 KB | Display | PDB format |
PDBx/mmJSON format | 7dzv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dz/7dzv ftp://data.pdbj.org/pub/pdb/validation_reports/dz/7dzv | HTTPS FTP |
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-Related structure data
Related structure data | 7dztSC 7dzuC 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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Unit cell |
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-Components
#1: Protein | Mass: 28478.676 Da / Num. of mol.: 1 / Fragment: PET hydrolase / Mutation: E186A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhizobacter gummiphilus (bacteria) / Strain: NS21 / Gene: A4W93_05950 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta gami-B / References: UniProt: A0A1W6L588 | ||||
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#2: Chemical | #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: 2.66 Å3/Da / Density % sol: 53.8 % / Mosaicity: 0.647 ° |
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 7 / Details: Sodium citrate tribasic, Tris, NaCl |
-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 17, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.6→50 Å / Num. obs: 40798 / % possible obs: 99.4 % / Redundancy: 12.4 % / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.028 / Rrim(I) all: 0.1 / Χ2: 3.097 / Net I/σ(I): 14.2 / Num. measured all: 505354 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7DZT Resolution: 1.6→30.25 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / SU B: 0.939 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 89.08 Å2 / Biso mean: 12.936 Å2 / Biso min: 2.95 Å2
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Refinement step | Cycle: final / Resolution: 1.6→30.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.639 Å / Rfactor Rfree error: 0
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