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- PDB-6teg: Crystal structure of monooxygenase RutA complexed with uracil and... -

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Basic information

Entry
Database: PDB / ID: 6teg
TitleCrystal structure of monooxygenase RutA complexed with uracil and 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 / 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 / OXYGEN MOLECULE / URACIL / Pyrimidine monooxygenase RutA
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
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
DepositionNov 11, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
AAA: Pyrimidine monooxygenase RutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8085
Polymers40,1111
Non-polymers6964
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-9 kcal/mol
Surface area13590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.863, 87.863, 96.253
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: 40111.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / 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-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-URA / URACIL


Mass: 112.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#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: 2.67 Å3/Da / Density % sol: 54 %
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, 1mM Uracil

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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→48.13 Å / Num. obs: 40105 / % possible obs: 99.5 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 23.5
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.35 / Num. unique obs: 5678

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WAN

5wan


Resolution: 1.8→43.97 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.052 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.106
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.212 2076 5.18 %
Rwork0.1689 --
all0.171 --
obs-40074 99.437 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.804 Å2
Baniso -1Baniso -2Baniso -3
1-0.127 Å20.063 Å20 Å2
2--0.127 Å20 Å2
3----0.411 Å2
Refinement stepCycle: LAST / Resolution: 1.8→43.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2618 0 46 161 2825
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132731
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172452
X-RAY DIFFRACTIONr_angle_refined_deg1.8831.6583709
X-RAY DIFFRACTIONr_angle_other_deg1.5181.5815671
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1095336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.31222.148135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20115421
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0771515
X-RAY DIFFRACTIONr_chiral_restr0.1010.2351
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023070
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02609
X-RAY DIFFRACTIONr_nbd_refined0.220.2484
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.22256
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21366
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.21138
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2115
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1890.26
X-RAY DIFFRACTIONr_nbd_other0.1620.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1860.211
X-RAY DIFFRACTIONr_mcbond_it2.783.1611350
X-RAY DIFFRACTIONr_mcbond_other2.7783.1571349
X-RAY DIFFRACTIONr_mcangle_it3.5344.7171684
X-RAY DIFFRACTIONr_mcangle_other3.5344.7221685
X-RAY DIFFRACTIONr_scbond_it4.63.7691381
X-RAY DIFFRACTIONr_scbond_other4.5863.7651377
X-RAY DIFFRACTIONr_scangle_it6.6085.4692025
X-RAY DIFFRACTIONr_scangle_other6.5995.4622020
X-RAY DIFFRACTIONr_lrange_it7.80837.9953125
X-RAY DIFFRACTIONr_lrange_other7.77437.7313100
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.2421290.2152673X-RAY DIFFRACTION95.2413
1.847-1.8970.2321640.1912710X-RAY DIFFRACTION98.9669
1.897-1.9520.2151590.1752609X-RAY DIFFRACTION100
1.952-2.0120.2371130.1652580X-RAY DIFFRACTION100
2.012-2.0780.2041160.1672527X-RAY DIFFRACTION100
2.078-2.1510.2111170.1662442X-RAY DIFFRACTION99.9609
2.151-2.2320.191220.1672328X-RAY DIFFRACTION99.9592
2.232-2.3230.1871220.1612247X-RAY DIFFRACTION100
2.323-2.4270.226920.1652153X-RAY DIFFRACTION99.7335
2.427-2.5450.2331150.1742075X-RAY DIFFRACTION99.9544
2.545-2.6820.2021090.1671968X-RAY DIFFRACTION99.8078
2.682-2.8450.2241060.1681869X-RAY DIFFRACTION99.7979
2.845-3.0410.2331070.181764X-RAY DIFFRACTION99.8399
3.041-3.2840.2171150.1761613X-RAY DIFFRACTION100
3.284-3.5970.218990.1741508X-RAY DIFFRACTION99.7517
3.597-4.020.166770.141379X-RAY DIFFRACTION100
4.02-4.640.171710.1371222X-RAY DIFFRACTION99.6916
4.64-5.6780.219670.1711017X-RAY DIFFRACTION98.9051
5.678-8.0070.294510.214824X-RAY DIFFRACTION98.9819
8-43.970.198250.196490X-RAY DIFFRACTION98.4704

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