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Yorodumi- PDB-8e8w: Crystal structure of SznF from Streptomyces achromogenes var. str... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8e8w | ||||||
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Title | Crystal structure of SznF from Streptomyces achromogenes var. streptozoticus NRRL 2697 mononuclear Fe(II) structure on the HDO cofactor assembly pathway | ||||||
Components | Cupin domain-containing diiron protein | ||||||
Keywords | OXIDOREDUCTASE / HDO / 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: 2.5 Å | ||||||
Authors | McBride, M.J. / Boal, A.K. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal structure of SznF from Streptomyces achromogenes var. streptozoticus NRRL 2697 mononuclear Fe(II) structure on the HDO cofactor assembly pathway Authors: McBride, M.J. / Boal, A.K. / Bollinger Jr., J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8e8w.cif.gz | 243.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8e8w.ent.gz | 154.9 KB | Display | PDB format |
PDBx/mmJSON format | 8e8w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8e8w_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 8e8w_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 8e8w_validation.xml.gz | 35.1 KB | Display | |
Data in CIF | 8e8w_validation.cif.gz | 49.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e8/8e8w ftp://data.pdbj.org/pub/pdb/validation_reports/e8/8e8w | HTTPS FTP |
-Related structure data
Related structure data | 6vzyS S: Starting model for refinement |
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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
#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) Gene: stzF, sznF Production host: Streptomyces achromogenes subsp. streptozoticus (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: 40.29 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 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: 21-ID-G / Wavelength: 0.9786 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jul 10, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 29840 / % possible obs: 94.7 % / Redundancy: 5.5 % / Biso Wilson estimate: 35.88 Å2 / CC1/2: 0.926 / Rmerge(I) obs: 0.157 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.5→2.54 Å / Num. unique obs: 1561 / CC1/2: 0.824 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6VZY Resolution: 2.5→45.79 Å / SU ML: 0.3641 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.7592 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: 35.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→45.79 Å
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Refine LS restraints |
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LS refinement shell |
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