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- PDB-6sgn: Crystal structure of monooxygenase RutA complexed with 2,4-dimeth... -

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Basic information

Entry
Database: PDB / ID: 6sgn
TitleCrystal structure of monooxygenase RutA complexed with 2,4-dimethoxypyrimidine.
ComponentsPyrimidine monooxygenase RutA
KeywordsFLAVOPROTEIN / monooxygenase / RutA / FMN / flavin-N5-oxide / bioengineering
Function / homology
Function and homology information


pyrimidine oxygenase / uracil oxygenase activity / pyrimidine nucleobase catabolic process / alkanesulfonate monooxygenase activity / alkanesulfonate catabolic process / thymine 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 / 2,4-dimethoxypyrimidine / Pyrimidine monooxygenase RutA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 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)40,5773
Polymers39,9801
Non-polymers5962
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-7 kcal/mol
Surface area13570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.136, 87.136, 95.541
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 / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-LD8 / 2,4-dimethoxypyrimidine


Mass: 140.140 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.62 Å3/Da / Density % sol: 53.03 %
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 2,4-Dimethoxypyrimidine

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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 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→47.77 Å / Num. obs: 14850 / % possible obs: 99.5 % / Redundancy: 5 % / CC1/2: 0.998 / Net I/σ(I): 11.2
Reflection shellResolution: 2.5→2.64 Å / Num. unique obs: 2101 / CC1/2: 0.615

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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: 2.501→43.606 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.927 / SU B: 10.359 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R: 0.333 / ESU R Free: 0.289
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2631 678 4.573 %
Rwork0.2007 --
all0.204 --
obs-14827 99.37 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 68.701 Å2
Baniso -1Baniso -2Baniso -3
1--0.556 Å2-0.278 Å20 Å2
2---0.556 Å20 Å2
3---1.804 Å2
Refinement stepCycle: LAST / Resolution: 2.501→43.606 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2587 0 41 13 2641
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122696
X-RAY DIFFRACTIONr_angle_refined_deg1.5311.6533660
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9235332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.45922.09134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.10215415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7661515
X-RAY DIFFRACTIONr_chiral_restr0.1110.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022082
X-RAY DIFFRACTIONr_nbd_refined0.2320.21263
X-RAY DIFFRACTIONr_nbtor_refined0.3180.21867
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.288
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2010.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1920.28
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.501-2.5660.324580.27597996.0185
2.566-2.6360.358560.271007100
2.636-2.7130.435470.27796999.9017
2.713-2.7960.353440.28297899.9023
2.796-2.8880.371340.26391499.6845
2.888-2.9890.256490.22589999.8946
2.989-3.1020.252360.21985899.6656
3.102-3.2280.303430.20183999.2126
3.228-3.3710.252340.19281099.7636
3.371-3.5350.27420.21974599.8731
3.535-3.7260.257230.20874899.8705
3.726-3.9520.274300.18705100
3.952-4.2240.156210.16265098.9676
4.224-4.5610.221430.16360399.0798
4.561-4.9940.241300.15356999.5017
4.994-5.5810.295180.19152899.8172
5.581-6.4380.264250.2345499.7917
6.438-7.8710.383140.21439599.5134
7.871-11.0710.207200.17131498.2353
11.0710.294110.23418697.5247

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