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- PDB-6alm: VioC L-arginine hydroxylase bound to Fe(II), L-arginine, and 2-OX... -

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Basic information

Entry
Database: PDB / ID: 6alm
TitleVioC L-arginine hydroxylase bound to Fe(II), L-arginine, and 2-OXO-GLUTARIC ACID
ComponentsAlpha-ketoglutarate-dependent L-arginine hydroxylase
KeywordsOXIDOREDUCTASE / hydroxylase / 2-oxo-glutarate / iron
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 / ARGININE / : / Alpha-ketoglutarate-dependent L-arginine hydroxylase
Similarity search - Component
Biological speciesStreptomyces vinaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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: 2017
Title: Visualizing the Reaction Cycle in an Iron(II)- and 2-(Oxo)-glutarate-Dependent Hydroxylase.
Authors: Mitchell, A.J. / Dunham, N.P. / Martinie, R.J. / Bergman, J.A. / Pollock, C.J. / Hu, K. / Allen, B.D. / Chang, W.C. / Silakov, A. / Bollinger, J.M. / Krebs, C. / Boal, A.K.
History
DepositionAug 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)43,6884
Polymers43,3101
Non-polymers3773
Water5,873326
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)87,3758
Polymers86,6212
Non-polymers7546
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4120 Å2
ΔGint-31 kcal/mol
Surface area26300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.336, 66.990, 62.665
Angle α, β, γ (deg.)90.000, 108.810, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-701-

HOH

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Components

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


Mass: 43310.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces vinaceus (bacteria) / Gene: vioC / Production host: Escherichia coli (E. coli) / References: UniProt: Q6WZB0, L-arginine hydroxylase
#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-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 1.84 Å3/Da / Density % sol: 33.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1 M 2-oxoglutarate, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 40551 / % possible obs: 97.4 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.02 / Rrim(I) all: 0.057 / Χ2: 0.714 / Net I/σ(I): 8.1 / Num. measured all: 311707
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.637.30.65719070.910.2550.7050.59992.5
1.63-1.667.50.58619540.9230.2260.6280.58894.4
1.66-1.697.60.5820220.9280.2230.6210.60395.7
1.69-1.727.70.47719550.9480.1820.5110.62196.4
1.72-1.767.70.39220030.9680.150.420.61796.6
1.76-1.87.80.33620190.9750.1280.3590.63196.8
1.8-1.857.70.2919870.980.1110.3110.65597.1
1.85-1.97.80.23920370.9860.0910.2560.70397.1
1.9-1.957.80.19420180.9910.0740.2070.82297.5
1.95-2.027.70.13120400.9950.050.140.68197.5
2.02-2.097.80.11720390.9970.0450.1250.82997.8
2.09-2.177.80.09720290.9970.0370.1030.72297.9
2.17-2.277.70.08420170.9980.0320.090.85898.2
2.27-2.397.80.06720430.9980.0260.0720.75298.2
2.39-2.547.70.05820490.9990.0220.0630.74998.5
2.54-2.747.70.04820740.9990.0180.0510.76198.7
2.74-3.017.70.03820420.9990.0150.0410.7699
3.01-3.457.70.0320890.9990.0120.0320.77499.2
3.45-4.347.70.023210310.0090.0250.77699.4
4.34-507.40.021212410.0080.0230.75499.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.22data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WBO

2wbo


Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.247 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.106
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2311 2050 5.1 %RANDOM
Rwork0.1977 ---
obs0.1993 38492 97.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 69.17 Å2 / Biso mean: 20.377 Å2 / Biso min: 11.95 Å2
Baniso -1Baniso -2Baniso -3
1-1.15 Å20 Å2-2.09 Å2
2---0.09 Å20 Å2
3---0.29 Å2
Refinement stepCycle: final / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2647 0 23 326 2996
Biso mean--21.37 27.92 -
Num. residues----338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0192737
X-RAY DIFFRACTIONr_bond_other_d0.0010.022597
X-RAY DIFFRACTIONr_angle_refined_deg0.9471.9563722
X-RAY DIFFRACTIONr_angle_other_deg0.69235921
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2085339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.7121.786140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.31415424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0461540
X-RAY DIFFRACTIONr_chiral_restr0.0520.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213160
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02680
LS refinement shellResolution: 1.598→1.64 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 148 -
Rwork0.249 2679 -
all-2827 -
obs--91.85 %

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