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- PDB-7enb: iron and alpha-ketoglutarate-dependent endoperoxidase NvfI with d... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7enb | ||||||
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Title | iron and alpha-ketoglutarate-dependent endoperoxidase NvfI with different conformation | ||||||
![]() | NvfI | ||||||
![]() | OXIDOREDUCTASE / Novofumigatonin / endoperoxidase | ||||||
Function / homology | : / Chem-H3X / N-OXALYLGLYCINE![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mori, T. / Abe, I. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 162.5 KB | Display | ![]() |
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PDB format | ![]() | 100.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 24.1 KB | Display | |
Data in CIF | ![]() | 34.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7de2SC ![]() 7emzC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() Production host: ![]() ![]() #2: Chemical | ChemComp-H3X / | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.89 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop Details: 50 mM HEPES pH 7.5, containing 20% PEG3350, 20 mM alpha-KG, 100 mM NaSCN |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 27, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→47.85 Å / Num. obs: 26939 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 28.27 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.178 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2619 / CC1/2: 0.729 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7DE2 Resolution: 2.3→45.62 Å / SU ML: 0.2549 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.7308 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: 29.99 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→45.62 Å
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Refine LS restraints |
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LS refinement shell |
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