+Open data
-Basic information
Entry | Database: PDB / ID: 7wpy | ||||||
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Title | AndA_M119A_N121V variant | ||||||
Components | Dioxygenase andA | ||||||
Keywords | OXIDOREDUCTASE / non heme iron 2-oxoglutarate dependent dioxygenase / meroterpenoid | ||||||
Function / homology | Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / terpenoid biosynthetic process / dioxygenase activity / metal ion binding / : / Dioxygenase andA Function and homology information | ||||||
Biological species | Aspergillus stellatus (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Mori, T. / Chen, H. / Abe, I. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: AndA_M119A_N121V variant Authors: Mori, T. / Chen, H. / Abe, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wpy.cif.gz | 272.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wpy.ent.gz | 174.6 KB | Display | PDB format |
PDBx/mmJSON format | 7wpy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wpy_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 7wpy_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 7wpy_validation.xml.gz | 39.7 KB | Display | |
Data in CIF | 7wpy_validation.cif.gz | 56.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wp/7wpy ftp://data.pdbj.org/pub/pdb/validation_reports/wp/7wpy | HTTPS FTP |
-Related structure data
Related structure data | 5zm2S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33641.168 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus stellatus (mold) / Gene: andA / Production host: Escherichia coli (E. coli) References: UniProt: A0A097ZPD5, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor #2: Chemical | ChemComp-FE / #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: 2.13 Å3/Da / Density % sol: 36.52 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop / Details: 28% PEG3350, 0.2 M LiCl, 5% DMF |
-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: Dec 12, 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: 2.25→48.74 Å / Num. obs: 48937 / % possible obs: 99.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 33.3 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.088 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.25→2.32 Å / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4453 / CC1/2: 0.739 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ZM2 Resolution: 2.25→40.45 Å / SU ML: 0.2293 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.8985 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: 37.45 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→40.45 Å
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Refine LS restraints |
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LS refinement shell |
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