+Open data
-Basic information
Entry | Database: PDB / ID: 7wzx | ||||||
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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 | Function and homology information heme biosynthetic process / catalytic activity / 4 iron, 4 sulfur cluster binding / metal ion binding Similarity search - Function | ||||||
Biological species | Streptomyces spectabilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98001304567 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 | 7wzx.cif.gz | 173.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wzx.ent.gz | 112.7 KB | Display | PDB format |
PDBx/mmJSON format | 7wzx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wzx_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7wzx_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7wzx_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 7wzx_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wz/7wzx ftp://data.pdbj.org/pub/pdb/validation_reports/wz/7wzx | HTTPS FTP |
-Related structure data
Related structure data | 7wzvSC 7x0bC 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 36014.637 Da / Num. of mol.: 1 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 , 6 types, 91 molecules
#2: Chemical | #3: Chemical | ChemComp-SAM / | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-7PK / ( | #6: Chemical | #7: 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: 2.54 Å3/Da / Density % sol: 51.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.5 M Sodium cacodylate trihydrate (pH 6.0), 1.8 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: BL19U1 / Wavelength: 0.97846 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97846 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→44.63 Å / Num. obs: 26783 / % possible obs: 100 % / Redundancy: 37.9 % / Biso Wilson estimate: 34.0387505161 Å2 / CC1/2: 1 / Net I/σ(I): 42.3 |
Reflection shell | Resolution: 1.98→2.03 Å / Rmerge(I) obs: 0.963 / Num. unique obs: 1844 / CC1/2: 0.949 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7WZV Resolution: 1.98001304567→41.2158933488 Å / SU ML: 0.250812795788 / Cross valid method: FREE R-VALUE / σ(F): 1.35002947799 / Phase error: 24.4586368563 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: 49.3943035328 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.98001304567→41.2158933488 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: 2.63957130723 Å / Origin y: 36.4786141394 Å / Origin z: 2.53794544531 Å
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Refinement TLS group | Selection details: all |