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- PDB-6sgm: Crystal structure of monooxygenase RutA complexed with 4-Thiouracil. -

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Basic information

Entry
Database: PDB / ID: 6sgm
TitleCrystal structure of monooxygenase RutA complexed with 4-Thiouracil.
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 / thymine catabolic process / alkanesulfonate catabolic process / uracil 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 / 4-Thiouracil / Pyrimidine monooxygenase RutA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 5, 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)40,5653
Polymers39,9801
Non-polymers5842
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-7 kcal/mol
Surface area13400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.567, 87.567, 95.999
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#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
#2: 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
#3: Chemical ChemComp-LDB / 4-Thiouracil / 4-sulfanylidene-1~{H}-pyrimidin-2-one


Mass: 128.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4N2OS / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.66 Å3/Da / Density % sol: 53.72 %
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),1 mM FMN, 1 mM 4-Thiouracil

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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: Nov 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→48 Å / Num. obs: 29258 / % possible obs: 100 % / Redundancy: 19.8 % / CC1/2: 0.99 / Net I/σ(I): 22.1
Reflection shellResolution: 2→2.11 Å / Num. unique obs: 4194 / CC1/2: 0.953

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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: 2→43.822 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.696 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.156
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2454 1386 4.742 %
Rwork0.2027 --
all0.205 --
obs-29228 99.99 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.855 Å2
Baniso -1Baniso -2Baniso -3
1-0.144 Å20.072 Å20 Å2
2--0.144 Å20 Å2
3----0.466 Å2
Refinement stepCycle: LAST / Resolution: 2→43.822 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2587 0 39 99 2725
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122694
X-RAY DIFFRACTIONr_angle_refined_deg1.6981.6533658
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7395332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.21522.09134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.92815415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.41515
X-RAY DIFFRACTIONr_chiral_restr0.1260.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022082
X-RAY DIFFRACTIONr_nbd_refined0.2140.21250
X-RAY DIFFRACTIONr_nbtor_refined0.3170.21876
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2129
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1960.235
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0760.25
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.0520.289730.2222052100
2.052-2.1080.2771070.2121959100
2.108-2.1690.26780.1971959100
2.169-2.2360.2551020.1981853100
2.236-2.3090.285950.2191821100
2.309-2.390.301870.2231742100
2.39-2.480.272730.2111713100
2.48-2.5810.304890.2241624100
2.581-2.6960.275760.2151594100
2.696-2.8280.258890.2021487100
2.828-2.980.258610.2071449100
2.98-3.1610.289800.2171351100
3.161-3.3790.226590.2051284100
3.379-3.6490.262620.2031209100
3.649-3.9960.237780.1881088100
3.996-4.4660.191540.1711005100
4.466-5.1540.181250.168921100
5.154-6.3050.208370.217757100
6.305-8.8860.297350.231616100
8.8860.186260.21435899.2248

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