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Yorodumi- PDB-6vzy: Crystal structure of SznF from Streptomyces achromogenes var. str... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vzy | ||||||
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Title | Crystal structure of SznF from Streptomyces achromogenes var. streptozoticus NRRL 2697 with a diiron(II) central domain cofactor | ||||||
Components | Cupin domain-containing diiron protein | ||||||
Keywords | OXIDOREDUCTASE / diiron / N-oxygenase / N-methyl-L-arginine / heme oxygenase | ||||||
Function / homology | Function and homology information nitrosourea synthase / antibiotic biosynthetic process / monooxygenase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Streptomyces achromogenes subsp. streptozoticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å | ||||||
Authors | McBride, M.J. / Boal, A.K. | ||||||
Funding support | 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2021 Title: Structure and assembly of the diiron cofactor in the heme-oxygenase-like domain of the N -nitrosourea-producing enzyme SznF. Authors: McBride, M.J. / Pope, S.R. / Hu, K. / Okafor, C.D. / Balskus, E.P. / Bollinger Jr., J.M. / Boal, A.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vzy.cif.gz | 240.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vzy.ent.gz | 161.7 KB | Display | PDB format |
PDBx/mmJSON format | 6vzy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vzy_validation.pdf.gz | 255.6 KB | Display | wwPDB validaton report |
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Full document | 6vzy_full_validation.pdf.gz | 255.5 KB | Display | |
Data in XML | 6vzy_validation.xml.gz | 1.2 KB | Display | |
Data in CIF | 6vzy_validation.cif.gz | 11.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vz/6vzy ftp://data.pdbj.org/pub/pdb/validation_reports/vz/6vzy | HTTPS FTP |
-Related structure data
Related structure data | 6xcvC 6m9rS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 56042.543 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces achromogenes subsp. streptozoticus (bacteria) Strain: NRRL 2697 / Gene: stzF, sznF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A411MR89 #2: Chemical | ChemComp-FE2 / #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: 2.06 Å3/Da / Density % sol: 40.3 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 16% PEG4000, 0.1 M magnesium chloride, 0.1 M Tris, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03319 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 13, 2019 |
Radiation | Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03319 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→50 Å / Num. obs: 109965 / % possible obs: 96.8 % / Redundancy: 5.8 % / Biso Wilson estimate: 14.43 Å2 / CC1/2: 0.996 / Net I/σ(I): 23.6 |
Reflection shell | Resolution: 1.66→1.69 Å / Num. unique obs: 109902 / CC1/2: 0.677 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6M9R Resolution: 1.66→36.42 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34
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Displacement parameters | Biso mean: 18.14 Å2 | ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.66→36.42 Å
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LS refinement shell | Resolution: 1.66→1.72 Å
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