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- PDB-9eqf: Crystal structure of the L-arginine hydroxylase VioC MeHis316, bo... -

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Basic information

Entry
Database: PDB / ID: 9eqf
TitleCrystal structure of the L-arginine hydroxylase VioC MeHis316, bound to Fe(II), L-arginine, and succinate
ComponentsAlpha-ketoglutarate-dependent L-arginine hydroxylase
KeywordsOXIDOREDUCTASE / 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
Arginine beta-hydroxylase, Fe2/alpha-ketoglutarate-dependent / : / Clavaminate synthase-like / TauD/TfdA-like domain / Taurine catabolism dioxygenase TauD, TfdA family / Taurine dioxygenase TauD-like superfamily
Similarity search - Domain/homology
ARGININE / : / DI(HYDROXYETHYL)ETHER / SUCCINIC ACID / Alpha-ketoglutarate-dependent L-arginine hydroxylase
Similarity search - Component
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsHardy, F.J.
Funding supportEuropean Union, United Kingdom, 3items
OrganizationGrant numberCountry
European Research Council (ERC)757991European Union
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M027023/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/W524347/1 United Kingdom
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
DepositionMar 21, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-ketoglutarate-dependent L-arginine hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8416
Polymers43,3231
Non-polymers5175
Water7,080393
1
A: Alpha-ketoglutarate-dependent L-arginine hydroxylase
hetero molecules

A: Alpha-ketoglutarate-dependent L-arginine hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,68212
Polymers86,6472
Non-polymers1,03510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)81.145, 67.107, 62.945
Angle α, β, γ (deg.)90.000, 109.221, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alpha-ketoglutarate-dependent L-arginine hydroxylase / Viomycin biosynthesis protein C


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 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.87 Å3/Da / Density % sol: 34.14 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Oct 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 1.6→1.64 Å / Mean I/σ(I) obs: 1.86 / Num. unique obs: 2681 / CC1/2: 0.922 / % possible all: 96.09

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
DIALSdata reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.1868 2082 4.96 %
Rwork0.1578 39868 -
obs0.1593 41950 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.31 Å2
Refinement stepCycle: LAST / Resolution: 1.6→38.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2628 0 32 393 3053
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00472869
X-RAY DIFFRACTIONf_angle_d0.80983920
X-RAY DIFFRACTIONf_chiral_restr0.0489422
X-RAY DIFFRACTIONf_plane_restr0.0096532
X-RAY DIFFRACTIONf_dihedral_angle_d14.80051102
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.26261100.23632568X-RAY DIFFRACTION96.09
1.64-1.680.2841490.21342577X-RAY DIFFRACTION98.45
1.68-1.720.22181450.19552670X-RAY DIFFRACTION99.96
1.72-1.770.2341490.18392643X-RAY DIFFRACTION99.89
1.77-1.830.23541130.19432668X-RAY DIFFRACTION99.96
1.83-1.90.21871350.18832662X-RAY DIFFRACTION99.96
1.9-1.970.20361370.16252689X-RAY DIFFRACTION99.96
1.97-2.060.18251460.15312615X-RAY DIFFRACTION100
2.06-2.170.181430.15752694X-RAY DIFFRACTION99.93
2.17-2.310.18531540.15552642X-RAY DIFFRACTION100
2.31-2.490.18611240.14832680X-RAY DIFFRACTION100
2.49-2.740.18371540.14462658X-RAY DIFFRACTION100
2.74-3.130.18821320.15522681X-RAY DIFFRACTION99.96
3.13-3.940.17171450.13932686X-RAY DIFFRACTION100
3.94-38.480.16251460.15272735X-RAY DIFFRACTION99.93

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