+Open data
-Basic information
Entry | Database: PDB / ID: 7wzv | ||||||
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Title | The structure of a Twitch Radical SAM Dehydrogenase SpeY | ||||||
Components | 4Fe-4S cluster-binding domain-containing protein | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Twitch Radical SAM Dehydrogenase / Spectinomycin / X-ray crystallography | ||||||
Function / homology | Function and homology information catalytic activity / 4 iron, 4 sulfur cluster binding / metal ion binding Similarity search - Function | ||||||
Biological species | Streptomyces spectabilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.89931293521 Å | ||||||
Authors | Zhou, J.H. / Hou, X.L. | ||||||
Funding support | 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2022 Title: Dioxane Bridge Formation during the Biosynthesis of Spectinomycin Involves a Twitch Radical S -Adenosyl Methionine Dehydrogenase That May Have Evolved from an Epimerase. Authors: Zhang, J. / Hou, X. / Chen, Z. / Ko, Y. / Ruszczycky, M.W. / Chen, Y. / 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 | 7wzv.cif.gz | 315.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wzv.ent.gz | 213.6 KB | Display | PDB format |
PDBx/mmJSON format | 7wzv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wz/7wzv ftp://data.pdbj.org/pub/pdb/validation_reports/wz/7wzv | HTTPS FTP |
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-Related structure data
Related structure data | 7wzxC 7x0bC 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 36014.637 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces spectabilis (bacteria) / Gene: speY, FH965_34950 / Production host: Escherichia coli (E. coli) / References: UniProt: A8WEZ7 |
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-Non-polymers , 9 types, 390 molecules
#2: Chemical | ChemComp-SF4 / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-NA / #7: Chemical | ChemComp-GOL / #8: Chemical | ChemComp-CL / | #9: Chemical | ChemComp-EDO / | #10: Water | ChemComp-HOH / | |
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-Details
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: 2.45 Å3/Da / Density % sol: 49.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.5 M Sodium cacodylate trihydrate (pH 6.5), 1.7 M Ammonium sulfate and 0.05 M Magnesium acetate tetrahydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97917 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 18, 2020 |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97917 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→70.77 Å / Num. obs: 53042 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.999 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.89→2 Å / Num. unique obs: 7642 / CC1/2: 0.79 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.89931293521→70.7643857242 Å / SU ML: 0.240473563064 / Cross valid method: THROUGHOUT / σ(F): 1.32609457704 / Phase error: 25.1162430572 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: 36.2001153623 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.89931293521→70.7643857242 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -4.07118898352 Å / Origin y: 16.4696925026 Å / Origin z: -27.1929538399 Å
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Refinement TLS group | Selection details: all |