+Open data
-Basic information
Entry | Database: PDB / ID: 7eyr | ||||||
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Title | Fe(II)/(alpha)ketoglutarate-dependent dioxygenase SptF apo | ||||||
Components | 2-oxoglutarate/Fe(II)-dependent dioxygenase SptF | ||||||
Keywords | OXIDOREDUCTASE / alpha-ketoglutarate dependent dioxygenase / meroterpenoid | ||||||
Function / homology | Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / dioxygenase activity / metal ion binding / : / 2-oxoglutarate/Fe(II)-dependent dioxygenase SptF Function and homology information | ||||||
Biological species | Aspergillus sp. (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å | ||||||
Authors | Tao, H. / Mori, T. / Abe, I. | ||||||
Citation | Journal: Nat Commun / Year: 2022 Title: Molecular insights into the unusually promiscuous and catalytically versatile Fe(II)/ alpha-ketoglutarate-dependent oxygenase SptF. Authors: Tao, H. / Mori, T. / Chen, H. / Lyu, S. / Nonoyama, A. / Lee, S. / Abe, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7eyr.cif.gz | 241.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7eyr.ent.gz | 189.7 KB | Display | PDB format |
PDBx/mmJSON format | 7eyr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7eyr_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 7eyr_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 7eyr_validation.xml.gz | 43.4 KB | Display | |
Data in CIF | 7eyr_validation.cif.gz | 61.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ey/7eyr ftp://data.pdbj.org/pub/pdb/validation_reports/ey/7eyr | HTTPS FTP |
-Related structure data
Related structure data | 7eysC 7eytC 7eyuC 7eywC 7fcbC 5zm2S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33843.184 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus sp. (mold) / Gene: sptF / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6J4CX17 #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: 1.96 Å3/Da / Density % sol: 37.14 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop Details: 0.27 M magnesium chloride, 21% w/v PEG 3350, 1.5% trimethylamine N-oxide dihydrate |
-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 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 9, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.12→48.57 Å / Num. obs: 56744 / % possible obs: 97.6 % / Redundancy: 5.4 % / Biso Wilson estimate: 20.74 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.098 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.12→2.18 Å / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 4456 / CC1/2: 0.927 / % possible all: 93.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ZM2 Resolution: 2.12→46.57 Å / SU ML: 0.2703 / Cross valid method: FREE R-VALUE / σ(F): 1.25 / Phase error: 27.9366 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: 25.81 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.12→46.57 Å
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Refine LS restraints |
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LS refinement shell |
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