+Open data
-Basic information
Entry | Database: PDB / ID: 7x0b | ||||||
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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 / Spectinomycin / Twitch Radical SAM Dehydrogenase / Epimerase | ||||||
Function / homology | Radical SAM superfamily / Radical SAM / catalytic activity / 4 iron, 4 sulfur cluster binding / Aldolase-type TIM barrel / metal ion binding / S-ADENOSYLMETHIONINE / IRON/SULFUR CLUSTER / 4Fe-4S cluster-binding domain-containing protein Function and homology information | ||||||
Biological species | Streptomyces spectabilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02027524648 Å | ||||||
Authors | Hou, X.L. / Zhou, J.H. | ||||||
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 | 7x0b.cif.gz | 322.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7x0b.ent.gz | 215.2 KB | Display | PDB format |
PDBx/mmJSON format | 7x0b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x0/7x0b ftp://data.pdbj.org/pub/pdb/validation_reports/x0/7x0b | HTTPS FTP |
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-Related structure data
Related structure data | 7wzvSC 7wzxC S: Starting model for refinement 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: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 2 - 300 / Label seq-ID: 22 - 320
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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 , 7 types, 288 molecules
#2: Chemical | ChemComp-SF4 / #3: Chemical | #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-GOL / #6: Chemical | #7: Chemical | ChemComp-NA / | #8: 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: 2.28 Å3/Da / Density % sol: 46.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.5 M Sodium cacodylate trihydrate (pH 6.5), 1.8 M Ammonium sulfate and 0.15 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: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→50 Å / Num. obs: 43975 / % possible obs: 99.9 % / Redundancy: 12.8 % / Biso Wilson estimate: 23.6981167031 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.172 |
Reflection shell | Resolution: 2.02→2.05 Å / Num. unique obs: 43975 / CC1/2: 0.722 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7WZV Resolution: 2.02027524648→35.9348943832 Å / SU ML: 0.252689238447 / Cross valid method: FREE R-VALUE / σ(F): 1.34479052676 / Phase error: 27.4294657737 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: 29.7303697378 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.02027524648→35.9348943832 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: -3.71340669681 Å / Origin y: 16.5125369526 Å / Origin z: 134.01268667 Å
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Refinement TLS group | Selection details: all |