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Yorodumi- PDB-9eqf: Crystal structure of the L-arginine hydroxylase VioC MeHis316, bo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9eqf | ||||||||||||
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Title | Crystal structure of the L-arginine hydroxylase VioC MeHis316, bound to Fe(II), L-arginine, and succinate | ||||||||||||
Components | Alpha-ketoglutarate-dependent L-arginine hydroxylase | ||||||||||||
Keywords | OXIDOREDUCTASE / non canonical amino acid / hydroxylate / 2OG oxygenase | ||||||||||||
Function / homology | Function and homology information L-arginine hydroxylase / 2-oxoglutarate, L-arginine oxygenase (succinate-forming) activity / 2-oxoglutarate-dependent dioxygenase activity / antibiotic biosynthetic process / iron ion binding / membrane Similarity search - Function | ||||||||||||
Biological species | synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||||||||
Authors | Hardy, F.J. | ||||||||||||
Funding support | European Union, United Kingdom, 3items
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Citation | Journal: Acs Catalysis / Year: 2024 Title: Probing Ferryl Reactivity in a Nonheme Iron Oxygenase Using an Expanded Genetic Code. Authors: Hardy, F.J. / Quesne, M.G. / Gerard, E.F. / Zhao, J. / Ortmayer, M. / Taylor, C.J. / Ali, H.S. / Slater, J.W. / Levy, C.W. / Heyes, D.J. / Bollinger Jr., J.M. / de Visser, S.P. / Green, A.P. #1: Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams / Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9eqf.cif.gz | 189.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9eqf.ent.gz | 120.6 KB | Display | PDB format |
PDBx/mmJSON format | 9eqf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9eqf_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 9eqf_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 9eqf_validation.xml.gz | 19 KB | Display | |
Data in CIF | 9eqf_validation.cif.gz | 29.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eq/9eqf ftp://data.pdbj.org/pub/pdb/validation_reports/eq/9eqf | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 43323.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Gene: vioC / Production host: Escherichia coli (E. coli) / References: UniProt: Q6WZB0, L-arginine hydroxylase |
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-Non-polymers , 6 types, 398 molecules
#2: Chemical | ChemComp-FE2 / |
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#3: Chemical | ChemComp-SIN / |
#4: Chemical | ChemComp-ARG / |
#5: Chemical | ChemComp-EDO / |
#6: Chemical | ChemComp-PEG / |
#7: Water | ChemComp-HOH / |
-Details
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: 1.87 Å3/Da / Density % sol: 34.14 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: final concentration of 10 mg ml-1 protein, in 20 mM HEPES buffer pH 7.5 containing 0.4 mM ammonium iron(II) sulphate hexahydrate, 2 mM L-arginine and 2 mM succinate, mixed 1:1 volume with 0. ...Details: final concentration of 10 mg ml-1 protein, in 20 mM HEPES buffer pH 7.5 containing 0.4 mM ammonium iron(II) sulphate hexahydrate, 2 mM L-arginine and 2 mM succinate, mixed 1:1 volume with 0.02 M magnesium chloride hexahydrate, 0.1 M HEPES, pH 7.5, containing 22 % (w/v) poly(acrylic acid sodium salt) 5100 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å |
Detector | Type: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Oct 16, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→38.48 Å / Num. obs: 41962 / % possible obs: 99.61 % / Redundancy: 6.6 % / Biso Wilson estimate: 17.87 Å2 / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 15.47 |
Reflection shell | Resolution: 1.6→1.64 Å / Mean I/σ(I) obs: 1.86 / Num. unique obs: 2681 / CC1/2: 0.922 / % possible all: 96.09 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→38.48 Å / SU ML: 0.1451 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.2544 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.31 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→38.48 Å
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Refine LS restraints |
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LS refinement shell |
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