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

ID or keywords:

Entry

Database: PDB / ID: 6tef

Title

Crystal structure of monooxygenase RutA complexed with dioxygen under 0.5 MPa / 5 bars of oxygen pressure.

Components

Pyrimidine monooxygenase RutA

Keywords

FLAVOPROTEIN /

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

Biological species

Escherichia coli K-12 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Saleem-Batcha, R. / Matthews, A. / Teufel, R.

Funding support

Germany, 2items

Citation

Journal: 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

Deposition	Nov 11, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 5, 2020	Provider: repository / Type: Initial release
Revision 1.1	May 6, 2020	Group: 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 1.2	Jan 24, 2024	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6tef.cif.gz	90.5 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/te/6tef ftp://data.pdbj.org/pub/pdb/validation_reports/te/6tef	HTTPS FTP

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Related structure data

Related structure data	6sggC 6sglC 6sgmC 6sgnC 6teeC 6tegC 5wanS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6sgm-d 6sgg-d 5wan-d 6teg-d 1ls5-2 2vbp-d 6sgn-d 6tzg-3 6hsj-2 5e8y-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#78 - Jun 2006 Luciferase similarity (3) #263 - Nov 2021 Acetohydroxyacid Synthase similarity (1) #41 - May 2003 Hemoglobin similarity (1) #159 - Mar 2013 Erythrocruorin similarity (1) #186 - Jun 2015 Receptor for Advanced Glycation End Products similarity (1) #206 - Feb 2017 Globin Evolution similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1)

Deposited unit

AAA: Pyrimidine monooxygenase RutA

hetero molecules

41 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	87.673, 87.673, 96.571
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21

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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, 207 molecules

#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: 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
#5: Chemical	ChemComp-OXY / OXYGEN MOLECULE / Oxygen Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O₂
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.67 Å³/Da / Density % sol: 53.95 %
Crystal grow	Temperature: 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

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 27, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.8→48.29 Å / Num. obs: 40277 / % possible obs: 100 % / Redundancy: 9.9 % / R_merge(I) obs: 0.08 / Net I/σ(I): 17.2
Reflection shell	Resolution: 1.8→1.9 Å / Num. unique obs: 5809 / CC_1/2: 0.84

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0257	refinement
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5WAN

5wan

Resolution: 1.8→43.875 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.956 / SU B: 2.032 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.099
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1963	2088	5.189 %
R_work	0.1598	-	-
all	0.162	-	-
obs	-	40237	99.963 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 27.675 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.105 Å²	0.053 Å²	0 Å²
2-	-	0.105 Å²	0 Å²
3-	-	-	-0.342 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→43.875 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2618	0	54	201	2873

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.013	2755
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	2477
X-RAY DIFFRACTION	r_angle_refined_deg	1.81	1.658	3745
X-RAY DIFFRACTION	r_angle_other_deg	1.538	1.581	5733
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.904	5	342
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.257	21.971	137
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.958	15	428
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.737	15	16
X-RAY DIFFRACTION	r_chiral_restr	0.095	0.2	354
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	3089
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	613
X-RAY DIFFRACTION	r_nbd_refined	0.214	0.2	520
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.184	0.2	2293
X-RAY DIFFRACTION	r_nbtor_refined	0.177	0.2	1375
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	1163
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.14	0.2	168
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.169	0.2	8
X-RAY DIFFRACTION	r_nbd_other	0.184	0.2	49
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.252	0.2	9
X-RAY DIFFRACTION	r_mcbond_it	2.479	2.617	1356
X-RAY DIFFRACTION	r_mcbond_other	2.478	2.613	1355
X-RAY DIFFRACTION	r_mcangle_it	3.215	3.907	1693
X-RAY DIFFRACTION	r_mcangle_other	3.214	3.912	1694
X-RAY DIFFRACTION	r_scbond_it	4.267	3.168	1399
X-RAY DIFFRACTION	r_scbond_other	4.265	3.168	1397
X-RAY DIFFRACTION	r_scangle_it	6.045	4.585	2049
X-RAY DIFFRACTION	r_scangle_other	6.044	4.586	2050
X-RAY DIFFRACTION	r_lrange_it	7.466	32.187	3234
X-RAY DIFFRACTION	r_lrange_other	7.424	31.719	3190

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.8-1.847	0.251	140	0.24	2783	X-RAY DIFFRACTION	100
1.847-1.897	0.248	165	0.225	2715	X-RAY DIFFRACTION	100
1.897-1.952	0.221	156	0.196	2621	X-RAY DIFFRACTION	100
1.952-2.012	0.228	116	0.165	2599	X-RAY DIFFRACTION	99.9264
2.012-2.078	0.21	112	0.17	2519	X-RAY DIFFRACTION	99.924
2.078-2.151	0.211	117	0.167	2421	X-RAY DIFFRACTION	99.9606
2.151-2.232	0.2	126	0.165	2338	X-RAY DIFFRACTION	100
2.232-2.323	0.19	126	0.152	2240	X-RAY DIFFRACTION	99.8312
2.323-2.427	0.202	90	0.152	2171	X-RAY DIFFRACTION	100
2.427-2.545	0.195	114	0.158	2076	X-RAY DIFFRACTION	100
2.545-2.682	0.188	109	0.153	1963	X-RAY DIFFRACTION	99.9518
2.682-2.845	0.214	100	0.155	1868	X-RAY DIFFRACTION	100
2.845-3.041	0.21	110	0.159	1747	X-RAY DIFFRACTION	100
3.041-3.284	0.199	114	0.156	1614	X-RAY DIFFRACTION	100
3.284-3.597	0.181	101	0.152	1518	X-RAY DIFFRACTION	100
3.597-4.02	0.168	77	0.14	1367	X-RAY DIFFRACTION	100
4.02-4.64	0.141	71	0.13	1232	X-RAY DIFFRACTION	99.8467
4.64-5.678	0.198	66	0.149	1035	X-RAY DIFFRACTION	100
5.678-8.007	0.242	53	0.186	825	X-RAY DIFFRACTION	100
8.007-43.875	0.211	25	0.199	497	X-RAY DIFFRACTION	99.4286

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