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- PDB-6y12: Arginine hydroxylase VioC in complex with (3S)-OH-Arg, succinate ... -

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Basic information

Entry
Database: PDB / ID: 6y12
TitleArginine hydroxylase VioC in complex with (3S)-OH-Arg, succinate and Fe after oxygen exposure using FT-SSX methods
ComponentsAlpha-ketoglutarate-dependent L-arginine hydroxylase
KeywordsOXIDOREDUCTASE / iron dependent oxygenase / Arginine hydroxylase
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
: / SUCCINIC ACID / (2S,3S)-3-HYDROXYARGININE / Alpha-ketoglutarate-dependent L-arginine hydroxylase
Similarity search - Component
Biological speciesStreptomyces vinaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsRabe, P. / Beale, J.H. / Lang, P.A. / Dirr, A.S. / Leissing, T.M. / Butryn, A. / Aller, P. / Kamps, J.J.A.G. / Axford, D. / McDonough, M.A. ...Rabe, P. / Beale, J.H. / Lang, P.A. / Dirr, A.S. / Leissing, T.M. / Butryn, A. / Aller, P. / Kamps, J.J.A.G. / Axford, D. / McDonough, M.A. / Orville, A.M. / Owen, R. / Schofield, C.J.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust106244/Z/14/Z United Kingdom
Medical Research Council (United Kingdom)MR/N002679/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/S50676X/1 United Kingdom
CitationJournal: Iucrj / Year: 2020
Title: Anaerobic fixed-target serial crystallography.
Authors: Rabe, P. / Beale, J.H. / Butryn, A. / Aller, P. / Dirr, A. / Lang, P.A. / Axford, D.N. / Carr, S.B. / Leissing, T.M. / McDonough, M.A. / Davy, B. / Ebrahim, A. / Orlans, J. / Storm, S.L.S. / ...Authors: Rabe, P. / Beale, J.H. / Butryn, A. / Aller, P. / Dirr, A. / Lang, P.A. / Axford, D.N. / Carr, S.B. / Leissing, T.M. / McDonough, M.A. / Davy, B. / Ebrahim, A. / Orlans, J. / Storm, S.L.S. / Orville, A.M. / Schofield, C.J. / Owen, R.L.
History
DepositionFeb 11, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)39,8454
Polymers39,4811
Non-polymers3643
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint-12 kcal/mol
Surface area13820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.369, 67.125, 63.984
Angle α, β, γ (deg.)90.000, 110.150, 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
Components on special symmetry positions
IDModelComponents
11A-696-

HOH

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Components

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


Mass: 39481.199 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 BL21(DE3) (bacteria) / References: UniProt: Q6WZB0, L-arginine hydroxylase
#2: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#3: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-ZZU / (2S,3S)-3-HYDROXYARGININE


Type: L-peptide linking / Mass: 190.200 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H14N4O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O
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: 2.1 Å3/Da / Density % sol: 41.51 %
Crystal growTemperature: 298 K / Method: batch mode / pH: 7.5 / Details: 0.05M MgCl2, 26% PEG550, 0.1M HEPES

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Data collection

DiffractionMean temperature: 293 K / Ambient temp details: room temperature / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96863 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2019
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 1.7→60.08 Å / Num. obs: 36065 / % possible obs: 99.92 % / Redundancy: 62.41 % / Biso Wilson estimate: 19.9016295827 Å2 / CC1/2: 0.949 / R split: 0.215 / Net I/σ(I): 34.19
Reflection shellResolution: 1.7→1.761 Å / Mean I/σ(I) obs: 2.34 / Num. unique obs: 3574 / CC1/2: 0.255 / R split: 0.841 / % possible all: 99.39
Serial crystallography measurementCollimation: KB mirrors / Source size: 49 µm2
Serial crystallography sample deliveryDescription: fixed target / Method: fixed target
Serial crystallography sample delivery fixed targetDescription: Aerobic chip / Sample holding: thin film mylar sandwich

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
GDAdata collection
DIALS1.8data reduction
DIALS1.8data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WBO

2wbo


Resolution: 1.7→60.07 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.336 / Phase error: 23.93
RfactorNum. reflection% reflection
Rfree0.21 1997 5.54 %
Rwork0.182 --
obs0.184 36050 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 29.05 Å2
Refinement stepCycle: LAST / Resolution: 1.7→60.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2497 0 22 203 2722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042648
X-RAY DIFFRACTIONf_angle_d0.6983618
X-RAY DIFFRACTIONf_chiral_restr0.045396
X-RAY DIFFRACTIONf_plane_restr0.004492
X-RAY DIFFRACTIONf_dihedral_angle_d10.56259150481575
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.701-1.740.361400.312404X-RAY DIFFRACTION99.3
1.74-1.790.331410.292410X-RAY DIFFRACTION99.73
1.79-1.840.321410.272404X-RAY DIFFRACTION100
1.84-1.90.281430.252436X-RAY DIFFRACTION100
1.9-1.970.261430.222442X-RAY DIFFRACTION100
1.97-2.050.231420.22417X-RAY DIFFRACTION100
2.05-2.140.231410.192398X-RAY DIFFRACTION100
2.14-2.250.231440.182442X-RAY DIFFRACTION100
2.25-2.40.221420.182429X-RAY DIFFRACTION100
2.4-2.580.21430.182448X-RAY DIFFRACTION100
2.58-2.840.21430.172429X-RAY DIFFRACTION100
2.84-3.250.211430.172433X-RAY DIFFRACTION100
3.25-4.10.171450.152465X-RAY DIFFRACTION100
4.1-60.070.1651460.162496X-RAY DIFFRACTION99.96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.716231637660.7126386358530.5563972905794.74749136402-1.075768054311.74929729268-0.0930956026839-0.305069728524-0.6319566693260.3204402856550.02821635604440.3390475897290.458330510528-0.01026210925350.104929157830.196428290729-0.052650697736-0.07673702366270.1413824809030.03228196954640.1253131553330.83459500011-16.443236606315.4269715645
20.236999576210.00603480224690.3906548982360.818489443672-0.3115841355071.950447986120.04116402900380.0110789642303-0.114373133478-0.05044148089020.0320246572520.04529733429660.1927252893990.0451591801134-0.05576558603860.206035083151-0.00919093309037-0.01482867198360.1436007649260.001891680583550.2088843654944.03574854115-11.61611368559.99665734058
30.72322462564-0.6368284262890.5180373711571.62850547566-0.3202224620661.461205011130.0231208685034-0.001462610884020.04581187999970.113314476444-0.0210175721561-0.189292328329-0.03540693536140.1262253037580.001425369242350.150552112095-0.01259251289160.005986460616150.1776088809380.01022651488640.17982801920412.2956267005-1.0379671757117.729835666
45.80625597037-6.881280067954.357233080629.37778146539-5.335482527423.850011222230.0128882829428-0.0514193870574-0.307344061348-0.09779947582370.05699431615040.4131524425820.060500553471-0.10019744606-0.1166298188110.1305367506150.00333451211680.03000486325940.150636856633-0.0272314938820.125825901678-7.3540049340911.858063976820.7209658477
58.53155262091-3.491655380670.7979631009515.37666998752-0.5055616953282.302711323280.01586616211210.2043928297730.5357073617720.169073416854-0.0527771975068-1.19122396118-0.1004555106590.7948716002790.05198007324260.312180057034-0.0299513293262-0.002604531659720.396826480987-0.0008634868484640.3887812283210.249841618416.969200836112.5820549175
64.889325575393.808612903090.7848883257988.705334575882.741420424752.74548243589-0.02155827670580.1416591793290.2017501849980.00272967313926-0.1003211295950.0476055088305-0.3673195028350.2494541679760.1217030826780.221849427433-0.003899741163970.01941459360690.1513991278920.03186204821540.103993299409-1.3545297334117.500826834314.8254064541
78.49901044434.12391878561-2.896206584367.79587585017-5.541681056717.70683484978-0.1082227796990.008185432248990.2820640755980.3148133118110.1256621604620.229835647902-0.394024609413-0.08997914313870.007514811993250.1775856567080.01671445855790.002629436823140.136528489544-0.05274173827290.125340857006-4.9344861290520.479287804222.9208931669
83.96415074543-2.868570584962.971852009423.44778825209-1.619324329812.53905645463-0.0405070193073-0.1203463420420.007934987147530.163249309144-0.006362925148550.0609724555990.0690171839425-0.008704102732130.05522979926480.1241313969-0.02429746023650.04310107534820.1248925254810.02658294598130.1281552949444.50670404553-1.4641618577825.2621569706
91.24765167927-1.198084271392.142253279893.62889997075-2.857429459373.809424308150.02250273873990.3431894543680.065754611695-0.307989937287-0.272299218862-0.264067863668-0.1874137185230.5954603492920.2411496717250.188871175770.01489224236430.04546570869060.2442699186770.01800283261460.17358870210111.2940574271.469505779945.25698749188
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 47 )
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 99 )
3X-RAY DIFFRACTION3chain 'A' and (resid 100 through 187 )
4X-RAY DIFFRACTION4chain 'A' and (resid 188 through 212 )
5X-RAY DIFFRACTION5chain 'A' and (resid 213 through 258 )
6X-RAY DIFFRACTION6chain 'A' and (resid 259 through 278 )
7X-RAY DIFFRACTION7chain 'A' and (resid 279 through 295 )
8X-RAY DIFFRACTION8chain 'A' and (resid 296 through 330 )
9X-RAY DIFFRACTION9chain 'A' and (resid 331 through 356 )

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