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- PDB-7vbq: Heterodimer structure of Fe(II)/(alpha)ketoglutarate-dependent di... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7vbq | ||||||
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Title | Heterodimer structure of Fe(II)/(alpha)ketoglutarate-dependent dioxygenase TlxIJ | ||||||
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![]() | OXIDOREDUCTASE / Fe(II)/(alpha)ketoglutarate-dependent dioxygenase / heterodimer | ||||||
Function / homology | : / N-OXALYLGLYCINE![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, X. / Awakawa, T. / Mori, T. / Abe, I. | ||||||
Funding support | 1items
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![]() | ![]() Title: Heterodimeric Non-heme Iron Enzymes in Fungal Meroterpenoid Biosynthesis. Authors: Li, X. / Awakawa, T. / Mori, T. / Ling, M. / Hu, D. / Wu, B. / 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 | ![]() | 135.7 KB | Display | ![]() |
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PDB format | ![]() | 99.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 24.7 KB | Display | |
Data in CIF | ![]() | 37 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7vbrC ![]() 5zm2S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 35905.406 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Protein | Mass: 31676.865 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
#3: Chemical | ChemComp-OGA / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.95 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop Details: 0.1M Tris-HCl (PH 7.2), 20% (w/v) PEG 3350, 200mM Calcium acetate |
-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: Jun 28, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→46.42 Å / Num. obs: 43789 / % possible obs: 99.2 % / Redundancy: 15.3 % / Biso Wilson estimate: 21.47 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.201 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.95→2 Å / Rmerge(I) obs: 1.456 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3021 / CC1/2: 0.831 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5zm2 Resolution: 1.95→46.42 Å / SU ML: 0.1801 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.602 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: 23.94 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→46.42 Å
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Refine LS restraints |
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LS refinement shell |
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