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Yorodumi- PDB-7kq3: Structure of isethionate sulfite-lyase from Bilophila wadsworthia... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7kq3 | |||||||||
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Title | Structure of isethionate sulfite-lyase from Bilophila wadsworthia with substrate isethionate bound | |||||||||
Components | Isethionate sulfite-lyase | |||||||||
Keywords | LYASE / glycyl radical enzyme / isethionate-sulfite lyase / carbon-sulfur bond cleavage / microbiome | |||||||||
Function / homology | Function and homology information Lyases; Carbon-sulfur lyases / alkanesulfonate catabolic process / lyase activity Similarity search - Function | |||||||||
Biological species | Bilophila wadsworthia | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.688 Å | |||||||||
Authors | Dawson, C.D. / Backman, L.R.F. / Drennan, C.L. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Cell Chem Biol / Year: 2021 Title: Molecular basis of C-S bond cleavage in the glycyl radical enzyme isethionate sulfite-lyase. Authors: Dawson, C.D. / Irwin, S.M. / Backman, L.R.F. / Le, C. / Wang, J.X. / Vennelakanti, V. / Yang, Z. / Kulik, H.J. / Drennan, C.L. / Balskus, E.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7kq3.cif.gz | 650.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kq3.ent.gz | 537.5 KB | Display | PDB format |
PDBx/mmJSON format | 7kq3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kq3_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7kq3_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7kq3_validation.xml.gz | 114.8 KB | Display | |
Data in CIF | 7kq3_validation.cif.gz | 160.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kq/7kq3 ftp://data.pdbj.org/pub/pdb/validation_reports/kq/7kq3 | HTTPS FTP |
-Related structure data
Related structure data | 7kq4C 5fauS 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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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: MET / End label comp-ID: MET / Auth seq-ID: 6 - 830 / Label seq-ID: 6 - 830
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-Components
#1: Protein | Mass: 94081.695 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bilophila wadsworthia (strain 3_1_6) (bacteria) Strain: 3_1_6 / Gene: islA, iseG, HMPREF0179_00639 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E5Y378, Lyases; Carbon-sulfur lyases #2: Chemical | ChemComp-8X3 / #3: 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: 2.59 Å3/Da / Density % sol: 52.47 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 0.16 M sodium bromide, 20% PEG 3350, and 10 mM sodium isethionate. Paraffin oil was used as a cryoprotectant. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 3, 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: 2.688→50 Å / Num. obs: 107420 / % possible obs: 98.9 % / Redundancy: 4.1 % / CC1/2: 0.969 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.6881→2.7186 Å / Num. unique obs: 10625 / CC1/2: 0.496 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5FAU Resolution: 2.688→49.223 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.92 / 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: 80.34 Å2 / Biso mean: 36.722 Å2 / Biso min: 20.34 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.688→49.223 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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