+Open data
-Basic information
Entry | Database: PDB / ID: 7vpb | ||||||
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Title | Crystal structure of a novel hydrolase in apo form | ||||||
Components | plastic degrading hydrolase Ple629 | ||||||
Keywords | HYDROLASE / plastic degradation | ||||||
Function / homology | ACETATE ION / 4-(2-hydroxyethylcarbamoyl)benzoic acid Function and homology information | ||||||
Biological species | unclassified Marinobacter (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å | ||||||
Authors | Wu, P. / Zhao, Y.P. / Li, Z.S. / Ingrid, M.C. / Lara, P. / Gao, J. / Han, X. / Li, Q. / Basak, O. / Liu, W.D. / Wei, R. | ||||||
Funding support | 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2022 Title: Structural insight and engineering of a plastic degrading hydrolase Ple629. Authors: Li, Z. / Zhao, Y. / Wu, P. / Wang, H. / Li, Q. / Gao, J. / Qin, H.M. / Wei, H. / Bornscheuer, U.T. / Han, X. / Wei, R. / Liu, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vpb.cif.gz | 126.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vpb.ent.gz | 95.3 KB | Display | PDB format |
PDBx/mmJSON format | 7vpb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vpb_validation.pdf.gz | 852.8 KB | Display | wwPDB validaton report |
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Full document | 7vpb_full_validation.pdf.gz | 859.8 KB | Display | |
Data in XML | 7vpb_validation.xml.gz | 27.6 KB | Display | |
Data in CIF | 7vpb_validation.cif.gz | 41.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vp/7vpb ftp://data.pdbj.org/pub/pdb/validation_reports/vp/7vpb | HTTPS FTP |
-Related structure data
Related structure data | 6sbnS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30291.225 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unclassified Marinobacter (bacteria) / Plasmid: pET-32a / Production host: Escherichia coli BL21(DE3) (bacteria) #2: Chemical | #3: Chemical | ChemComp-J1K / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.13 Å3/Da / Density % sol: 42.35 % / Mosaicity: 1.092 ° |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 20% PEG 8000, 0.2M calcium acelate, 0.1M sodium cacodylate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 4, 2021 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.68→30 Å / Num. obs: 56997 / % possible obs: 99.9 % / Redundancy: 11.2 % / Biso Wilson estimate: 15.89 Å2 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.044 / Rrim(I) all: 0.151 / Χ2: 0.728 / Net I/σ(I): 3.4 / Num. measured all: 639478 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6SBN Resolution: 1.68→23.44 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 18.76 / 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: 70.97 Å2 / Biso mean: 19.2942 Å2 / Biso min: 8.31 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.68→23.44 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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