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Yorodumi- PDB-8daj: Structure and Biochemistry of a Promiscuous Thermophilic Polyhydr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8daj | ||||||
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Title | Structure and Biochemistry of a Promiscuous Thermophilic Polyhydroxybutyrate Depolymerase from Lihuaxuella thermophilia | ||||||
Components | Esterase, PHB depolymerase family | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Bioplastic / Thermophile / Enzyme / polyhydroxyalkanoates | ||||||
Function / homology | Esterase, PHB depolymerase / Esterase PHB depolymerase / Alpha/Beta hydrolase fold / hydrolase activity / extracellular region / ISOPROPYL ALCOHOL / Esterase, PHB depolymerase family Function and homology information | ||||||
Biological species | Lihuaxuella thermophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.2 Å | ||||||
Authors | Thomas, G.M. / Quirk, S. / Huard, D.J.E. / Lieberman, R.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: Protein Sci. / Year: 2022 Title: Bioplastic degradation by a polyhydroxybutyrate depolymerase from a thermophilic soil bacterium. Authors: Thomas, G.M. / Quirk, S. / Huard, D.J.E. / Lieberman, R.L. #1: Journal: To Be Published Title: Structure and Biochemistry of a Promiscuous Thermophilic Polyhydroxybutyrate Depolymerase from Lihuaxuella thermophilia Authors: Thomas, G.M. / Quirk, S. / Huard, D.J.E. / Lieberman, R.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8daj.cif.gz | 94.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8daj.ent.gz | 59.7 KB | Display | PDB format |
PDBx/mmJSON format | 8daj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8daj_validation.pdf.gz | 3.7 MB | Display | wwPDB validaton report |
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Full document | 8daj_full_validation.pdf.gz | 3.7 MB | Display | |
Data in XML | 8daj_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 8daj_validation.cif.gz | 25.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/8daj ftp://data.pdbj.org/pub/pdb/validation_reports/da/8daj | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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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: 32441.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lihuaxuella thermophila (bacteria) / Gene: SAMN05444955_11823 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1H8IKU3 | ||||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-IPA / #4: 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 | Density Matthews: 1.95 Å3/Da / Density % sol: 36.82 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, sitting drop Details: 0.1M citrate pH 5.6, 18% propanol, and 20% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 9, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→36.93 Å / % possible obs: 97.69 % / Redundancy: 16.7 % / Biso Wilson estimate: 11.43 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.1339 / Rpim(I) all: 0.03208 / Rrim(I) all: 0.1378 / Net I/σ(I): 11.84 |
Reflection shell | Resolution: 1.2→1.243 Å / Redundancy: 6 % / Rmerge(I) obs: 0.4728 / Mean I/σ(I) obs: 1.51 / Num. unique obs: 6485 / CC1/2: 0.824 / CC star: 0.951 / Rpim(I) all: 0.1991 / Rrim(I) all: 0.5169 / % possible all: 81.8 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.2→36.93 Å / SU ML: 0.1227 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.3247 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.57 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→36.93 Å
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Refine LS restraints |
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LS refinement shell |
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