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Yorodumi- PDB-6vp5: Ethylene forming enzyme (EFE) D191E variant in complex with Fe(II... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vp5 | |||||||||
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Title | Ethylene forming enzyme (EFE) D191E variant in complex with Fe(II), L-arginine, and 2OG | |||||||||
Components | 2-oxoglutarate-dependent ethylene/succinate-forming enzyme | |||||||||
Keywords | OXIDOREDUCTASE / 2-oxo-glutarate / iron / reactant complex | |||||||||
Function / homology | Function and homology information 2-oxoglutarate dioxygenase (ethene-forming) / 2-oxoglutarate/L-arginine monooxygenase/decarboxylase (succinate-forming) / 2-oxoglutarate oxygenase/decarboxylase (ethylene-forming) activity / ethylene biosynthetic process / dioxygenase activity / metal ion binding Similarity search - Function | |||||||||
Biological species | Pseudomonas savastanoi pv. phaseolicola (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å | |||||||||
Authors | Davis, K.M. / Copeland, R.A. / Boal, A.K. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2021 Title: An Iron(IV)-Oxo Intermediate Initiating l-Arginine Oxidation but Not Ethylene Production by the 2-Oxoglutarate-Dependent Oxygenase, Ethylene-Forming Enzyme. Authors: Copeland, R.A. / Davis, K.M. / Shoda, T.K.C. / Blaesi, E.J. / Boal, A.K. / Krebs, C. / Bollinger Jr., J.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vp5.cif.gz | 310.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vp5.ent.gz | 243.8 KB | Display | PDB format |
PDBx/mmJSON format | 6vp5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vp/6vp5 ftp://data.pdbj.org/pub/pdb/validation_reports/vp/6vp5 | HTTPS FTP |
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-Related structure data
Related structure data | 6vp4C 5lsqS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 39592.645 Da / Num. of mol.: 4 / Mutation: D191E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas savastanoi pv. phaseolicola (bacteria) Gene: efe / Production host: Escherichia coli (E. coli) References: UniProt: P32021, 2-oxoglutarate dioxygenase (ethene-forming), 2-oxoglutarate/L-arginine monooxygenase/decarboxylase (succinate-forming) |
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-Non-polymers , 5 types, 1264 molecules
#2: Chemical | ChemComp-FE / #3: Chemical | ChemComp-AKG / #4: Chemical | ChemComp-ARG / #5: Chemical | ChemComp-B3P / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 2.4 Å3/Da / Density % sol: 48.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M Bis-Tris propane, 0.1-0.2 M sodium chloride, 24-30% PEG6000 PH range: 6.4-6.7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 30, 2018 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→49.52 Å / Num. obs: 105982 / % possible obs: 99.21 % / Redundancy: 7.5 % / Biso Wilson estimate: 16.6 Å2 / Rpim(I) all: 0.04034 / Net I/σ(I): 16.65 |
Reflection shell | Resolution: 1.97→2.04 Å / Num. unique obs: 9842 / Rpim(I) all: 0.2801 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5LSQ Resolution: 1.97→49.52 Å / SU ML: 0.1759 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.9225
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.51 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.97→49.52 Å
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Refine LS restraints |
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LS refinement shell |
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