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Yorodumi- PDB-7vob: The crystal structure of a Radical SAM Enzyme BlsE involved in th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7vob | ||||||
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Title | The crystal structure of a Radical SAM Enzyme BlsE involved in the Biosynthesis of Blasticidin S | ||||||
Components | Cytosylglucuronate decarboxylase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Radical SAM Enzyme / Dehydratase / Blasticidin S | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces griseochromogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.09224113188 Å | ||||||
Authors | Hou, X.L. / Zhou, J.H. | ||||||
Funding support | 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2022 Title: Radical S -Adenosyl Methionine Enzyme BlsE Catalyzes a Radical-Mediated 1,2-Diol Dehydration during the Biosynthesis of Blasticidin S. Authors: Lee, Y.H. / Hou, X. / Chen, R. / Feng, J. / Liu, X. / Ruszczycky, M.W. / Gao, J.M. / Wang, B. / Zhou, J. / Liu, H.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vob.cif.gz | 93.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vob.ent.gz | 62.1 KB | Display | PDB format |
PDBx/mmJSON format | 7vob.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vo/7vob ftp://data.pdbj.org/pub/pdb/validation_reports/vo/7vob | HTTPS FTP |
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-Related structure data
Related structure data | 7vocC C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules C
#1: Protein | Mass: 39967.023 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces griseochromogenes (bacteria) Gene: AVL59_19980 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1B1AYF2 |
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-Non-polymers , 5 types, 143 molecules
#2: Chemical | #3: Chemical | ChemComp-SAM / | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 6.64 Å3/Da / Density % sol: 81.48 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.1 M 2-(N-morpholino) ethanesulfonic acid monohydrate (MES) at pH 5.66, 3.0 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97921 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 9, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97921 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→66.57 Å / Num. obs: 63221 / % possible obs: 99.9 % / Redundancy: 26.7 % / Biso Wilson estimate: 48.3833276048 Å2 / CC1/2: 0.996 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.09→2.21 Å / Num. unique obs: 63221 / CC1/2: 0.996 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.09224113188→28.1760170488 Å / SU ML: 0.255279438098 / Cross valid method: FREE R-VALUE / σ(F): 1.36413587268 / Phase error: 24.4679440888 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 55.3103775108 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.09224113188→28.1760170488 Å
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Refine LS restraints |
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LS refinement shell |
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