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- PDB-6dax: X-ray crystal structure of VioC bound to Fe(II), L-homoarginine, ... -

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Basic information

Entry
Database: PDB / ID: 6dax
TitleX-ray crystal structure of VioC bound to Fe(II), L-homoarginine, and 2-oxoglutarate
ComponentsAlpha-ketoglutarate-dependent L-arginine hydroxylase
KeywordsOXIDOREDUCTASE / desaturase / hydroxylase / oxygenase / metalloenzyme / desaturation / hydroxylation / viomycin
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 / Clavaminate synthase-like / Double-stranded beta-helix / TauD/TfdA-like domain / Taurine catabolism dioxygenase TauD, TfdA family / Taurine dioxygenase TauD-like superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / L-HOMOARGININE / Alpha-ketoglutarate-dependent L-arginine hydroxylase
Similarity search - Component
Biological speciesStreptomyces vinaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsDunham, N.P. / Mitchell, A.J. / Boal, A.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM119707 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Two Distinct Mechanisms for C-C Desaturation by Iron(II)- and 2-(Oxo)glutarate-Dependent Oxygenases: Importance of alpha-Heteroatom Assistance.
Authors: Dunham, N.P. / Chang, W.C. / Mitchell, A.J. / Martinie, R.J. / Zhang, B. / Bergman, J.A. / Rajakovich, L.J. / Wang, B. / Silakov, A. / Krebs, C. / Boal, A.K. / Bollinger, J.M.
History
DepositionMay 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)37,8834
Polymers37,4931
Non-polymers3903
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area520 Å2
ΔGint-16 kcal/mol
Surface area14860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.376, 67.076, 62.646
Angle α, β, γ (deg.)90.000, 108.720, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 37493.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces vinaceus (bacteria) / References: UniProt: Q6WZB0, L-arginine hydroxylase
#2: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#3: Chemical ChemComp-HRG / L-HOMOARGININE / Homoarginine


Type: L-peptide linking / Mass: 188.228 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16N4O2
#4: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O

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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: 2.13 Å3/Da / Density % sol: 42.33 % / Mosaicity: 1.21 °
Crystal growTemperature: 293 K / Method: evaporation / pH: 8.5 / Details: 2-oxoglutarate, Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 15, 2015
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 33837 / % possible obs: 97.2 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.033 / Rrim(I) all: 0.063 / Χ2: 3.228 / Net I/σ(I): 11.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.733.30.43214900.890.2720.5120.7186.7
1.73-1.763.30.41715400.8990.260.4930.80689.4
1.76-1.793.40.3516150.9390.2170.4130.72392
1.79-1.833.50.34216380.9390.2110.4040.75295.2
1.83-1.873.50.30217290.9490.1860.3560.75997.8
1.87-1.913.60.24616910.9660.1510.2890.78599.3
1.91-1.963.70.2117400.9640.1280.2470.88999.9
1.96-2.023.70.17717460.9810.1080.2080.94799.9
2.02-2.073.80.16217000.9850.10.1911.197100
2.07-2.143.80.12817310.9880.0770.151.08299.9
2.14-2.223.80.11217500.9910.0670.1311.12399.9
2.22-2.313.80.09517370.9890.0570.1111.26399.9
2.31-2.413.80.07617500.9950.0460.0891.07399.9
2.41-2.543.80.06717310.9960.040.0791.15299.8
2.54-2.73.80.05317370.9970.0320.0621.16999.9
2.7-2.913.80.05517400.9980.0330.0641.46599.3
2.91-3.23.70.04217040.9980.0250.0492.44998
3.2-3.663.70.03216530.9970.020.0383.08294.7
3.66-4.613.70.02716420.9960.0170.0327.37193.5
4.61-503.60.04817730.9670.030.05734.18798.1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementResolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.333 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.115
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2238 1693 5 %RANDOM
Rwork0.2157 ---
obs0.2161 32080 96.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 82.54 Å2 / Biso mean: 26.603 Å2 / Biso min: 16.65 Å2
Baniso -1Baniso -2Baniso -3
1-1.98 Å20 Å2-3.43 Å2
2---0.68 Å20 Å2
3---0.83 Å2
Refinement stepCycle: final / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2647 0 24 87 2758
Biso mean--26.18 25.8 -
Num. residues----338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0192738
X-RAY DIFFRACTIONr_bond_other_d0.0030.022605
X-RAY DIFFRACTIONr_angle_refined_deg0.9911.9583723
X-RAY DIFFRACTIONr_angle_other_deg0.8053.0035929
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3185339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.39421.871139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.93715421
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8911539
X-RAY DIFFRACTIONr_chiral_restr0.0550.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213160
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02681
LS refinement shellResolution: 1.697→1.741 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 106 -
Rwork0.274 2093 -
all-2199 -
obs--84.54 %

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