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- PDB-6sgg: Crystal structure of monooxygenase RutA complexed with dioxygen u... -

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Basic information

Entry
Database: PDB / ID: 6sgg
TitleCrystal structure of monooxygenase RutA complexed with dioxygen under 1.5 MPa / 15 bars of oxygen pressure.
ComponentsPyrimidine monooxygenase RutA
KeywordsFLAVOPROTEIN / monooxygenase / RutA / FMN / flavin-N5-oxide / bioengineering
Function / homology
Function and homology information


pyrimidine oxygenase / uracil oxygenase activity / alkanesulfonate monooxygenase activity / pyrimidine nucleobase catabolic process / uracil catabolic process / thymine catabolic process / alkanesulfonate catabolic process / nitrogen utilization / monooxygenase activity
Similarity search - Function
Pyrimidine monooxygenase RutA / : / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / OXYGEN MOLECULE / Pyrimidine monooxygenase RutA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSaleem-Batcha, R. / Matthews, A. / Teufel, R.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationTE 931/2-1 Germany
German Research Foundation235777276/GRK1976 Germany
CitationJournal: Nat.Chem.Biol. / Year: 2020
Title: Aminoperoxide adducts expand the catalytic repertoire of flavin monooxygenases.
Authors: Matthews, A. / Saleem-Batcha, R. / Sanders, J.N. / Stull, F. / Houk, K.N. / Teufel, R.
History
DepositionAug 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
AAA: Pyrimidine monooxygenase RutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6575
Polymers39,9801
Non-polymers6774
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-15 kcal/mol
Surface area13650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.727, 87.727, 96.396
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules AAA

#1: Protein Pyrimidine monooxygenase RutA


Mass: 39980.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: rutA, ycdM, b1012, JW0997 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P75898, pyrimidine oxygenase

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Non-polymers , 5 types, 165 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.68 Å3/Da / Density % sol: 54.08 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 100 mM Bis-Tris pH 6.5, 1900 mM ammonium sulphate, 2-5% MPD (v/v) and 1 mM FMN

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→48.2 Å / Num. obs: 40260 / % possible obs: 100 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.8
Reflection shellResolution: 1.8→1.9 Å / Num. unique obs: 5800 / CC1/2: 0.861

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WAN

5wan


Resolution: 1.8→43.902 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.916 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.085
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1711 2077 5.17 %
Rwork0.1539 --
all0.155 --
obs-40174 99.856 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.803 Å2
Baniso -1Baniso -2Baniso -3
1-0.025 Å20.012 Å20 Å2
2--0.025 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.8→43.902 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2610 0 44 161 2815
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132731
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172456
X-RAY DIFFRACTIONr_angle_refined_deg1.8411.6583710
X-RAY DIFFRACTIONr_angle_other_deg1.5581.585685
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0065339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.64622.148135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.84915422
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.731515
X-RAY DIFFRACTIONr_chiral_restr0.0970.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023069
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02606
X-RAY DIFFRACTIONr_nbd_refined0.2080.2515
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.22293
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21355
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.21150
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2142
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2450.26
X-RAY DIFFRACTIONr_nbd_other0.160.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2120.29
X-RAY DIFFRACTIONr_mcbond_it2.3272.4461350
X-RAY DIFFRACTIONr_mcbond_other2.3132.4431349
X-RAY DIFFRACTIONr_mcangle_it3.0133.6521685
X-RAY DIFFRACTIONr_mcangle_other3.0133.6561686
X-RAY DIFFRACTIONr_scbond_it4.0032.9831381
X-RAY DIFFRACTIONr_scbond_other3.9962.9821379
X-RAY DIFFRACTIONr_scangle_it5.9724.3082023
X-RAY DIFFRACTIONr_scangle_other5.9714.3092024
X-RAY DIFFRACTIONr_lrange_it7.12429.8043174
X-RAY DIFFRACTIONr_lrange_other7.10129.4643141
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.8470.221350.201277299.4867
1.847-1.8970.2031510.18271399.7215
1.897-1.9520.1921590.169262899.7138
1.952-2.0120.2021410.163258699.9267
2.012-2.0780.1761560.162245099.8085
2.078-2.1510.2071040.163242899.8029
2.151-2.2320.191290.161232999.8781
2.232-2.3230.1891670.154219099.8729
2.323-2.4270.189980.1552161100
2.427-2.5450.1741130.152207499.9543
2.545-2.6820.162930.148198299.9518
2.682-2.8450.178880.1491880100
2.845-3.0410.174890.157177599.9464
3.041-3.2840.181000.1491624100
3.284-3.5970.1651070.1431504100
3.597-4.020.139770.1381381100
4.02-4.640.124680.1261225100
4.64-5.6780.139380.1481060100
5.678-8.0070.185460.17683399.6599
8.0070.202180.18750299.4264

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