+Open data
-Basic information
Entry | Database: PDB / ID: 7de2 | ||||||
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Title | iron and alpha-ketoglutarate-dependent endoperoxidase NvfI | ||||||
Components | NvfI | ||||||
Keywords | OXIDOREDUCTASE / Novofumigatonin / endoperoxidase / iron and alpha-ketoglutarate-dependent enzyme | ||||||
Function / homology | 2-OXOGLUTARIC ACID / : / Chem-H3X Function and homology information | ||||||
Biological species | Aspergillus novofumigatus IBT 16806 (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Zhai, R. / Mori, T. / Abe, I. | ||||||
Citation | Journal: Nat Commun / Year: 2021 Title: Molecular insights into the endoperoxide formation by Fe(II)/ alpha-KG-dependent oxygenase NvfI. Authors: Mori, T. / Zhai, R. / Ushimaru, R. / Matsuda, Y. / Abe, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7de2.cif.gz | 137.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7de2.ent.gz | 104 KB | Display | PDB format |
PDBx/mmJSON format | 7de2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7de2_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7de2_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7de2_validation.xml.gz | 26.5 KB | Display | |
Data in CIF | 7de2_validation.cif.gz | 38.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/7de2 ftp://data.pdbj.org/pub/pdb/validation_reports/de/7de2 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33959.164 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus novofumigatus IBT 16806 (mold) Production host: Escherichia coli (E. coli) #2: Chemical | #3: Chemical | ChemComp-H3X / | #4: Chemical | #5: 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: 2.19 Å3/Da / Density % sol: 43.77 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop Details: 50 mM Tris-HCl pH 7.0, 20% PEG3350, 20 mM alpha-ketoglutarate, 200 mM NaSCN, and 2 mM DTT |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 8, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→46.13 Å / Num. obs: 46701 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 20.46 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.141 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.9→1.94 Å / Rmerge(I) obs: 0.843 / Mean I/σ(I) obs: 3 / Num. unique obs: 3022 / CC1/2: 0.826 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→39.08 Å / SU ML: 0.1697 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.15 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: 25.47 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→39.08 Å
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Refine LS restraints |
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LS refinement shell |
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