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- PDB-5wan: Crystal Structure of a flavoenzyme RutA in the pyrimidine catabol... -

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Basic information

Entry
Database: PDB / ID: 5wan
TitleCrystal Structure of a flavoenzyme RutA in the pyrimidine catabolic pathway
ComponentsPyrimidine monooxygenase RutA
KeywordsOXIDOREDUCTASE / flavoenzyme
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 / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity
Similarity search - Function
Pyrimidine monooxygenase RutA / : / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / URACIL / Pyrimidine monooxygenase RutA / Pyrimidine monooxygenase RutA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.798 Å
AuthorsZhang, Y. / Mukherjee, T. / Abdelwahed, S. / Begley, T.P. / Ealick, S.E.
CitationJournal: J. Am. Chem. Soc. / Year: 2010
Title: Catalysis of a flavoenzyme-mediated amide hydrolysis.
Authors: Mukherjee, T. / Zhang, Y. / Abdelwahed, S. / Ealick, S.E. / Begley, T.P.
History
DepositionJun 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: 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

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Assembly

Deposited unit
A: Pyrimidine monooxygenase RutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,83110
Polymers44,6021
Non-polymers1,2299
Water4,810267
1
A: Pyrimidine monooxygenase RutA
hetero molecules

A: Pyrimidine monooxygenase RutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,66320
Polymers89,2052
Non-polymers2,45818
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area8280 Å2
ΔGint-117 kcal/mol
Surface area24440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.850, 87.850, 96.368
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Pyrimidine monooxygenase RutA


Mass: 44602.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rutA, BUE81_22975, BW690_24255 / Plasmid: pCA24N / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A1R1KFF4, UniProt: P75898*PLUS, pyrimidine oxygenase

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Non-polymers , 5 types, 276 molecules

#2: Chemical ChemComp-URA / URACIL


Mass: 112.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4N2O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O

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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: 2.41 Å3/Da / Density % sol: 48.89 %
Description: THE AUTHORS STATE THAT RESIDUAL ELECTRON DENSITY WAS IDENTIFIED IN THE ACTIVE SITE DURING THE FINAL STAGES OF REFINEMENT. THE ELECTRON DENSITY COULD BE EXPLAINED AS A MIXTURE OF THE ...Description: THE AUTHORS STATE THAT RESIDUAL ELECTRON DENSITY WAS IDENTIFIED IN THE ACTIVE SITE DURING THE FINAL STAGES OF REFINEMENT. THE ELECTRON DENSITY COULD BE EXPLAINED AS A MIXTURE OF THE SUBSTRATE URACIL AND THE PRODUCT 3-UREIDOACRYLATE, EVEN THOUGH NEITHER SUBSTRATE NOR PRODUCT WAS ADDED DURING PURIFICATION OR CRYSTALLIZATION. FOR CLARITY, ONLY THE URACIL WAS INCLUDED IN THE FINAL MODEL. AS MODELED, RUTA AND URACIL DO NOT SHOW EXPECTED INTERACTIONS BASED ON THE PROPOSED MECHANISM. IN PARTICULAR, FOR THE PEROXIDE TO ADD TO THE C4 CARBONYL OF URACIL, A HYDROGEN BOND FROM AN ACID INSTEAD OF A WATER MOLECULE IS EXPECTED. ALSO NEITHER N3 NOR THE C2 CARBONYL IS INVOLVED IN HYDROGEN BONDING FROM AN ACID AS REQUIRED FOR COLLAPSE OF THE TETRAHEDRAL INTERMEDIATE. THESE INTERACTIONS COULD CONCEIVABLY BE PROVIDED BY RESIDUES 274-292, WHICH ARE DISORDERED IN THE CRYSTAL STRUCTURE.
Mosaicity: 0.446 ° / Mosaicity esd: 0.004 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 2 mM FMN, 1.5 M ammonium sulfate, and 100 mM MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.798→40.707 Å / Num. obs: 39453 / % possible obs: 97.6 % / Redundancy: 5.4 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 19.4
Reflection shellResolution: 1.798→1.86 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 3198 / % possible all: 80

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
MrBUMPphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TVL and 1YW1

1tvl

1yw1


Resolution: 1.798→40.707 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.54
RfactorNum. reflection% reflection
Rfree0.1721 1972 5 %
Rwork0.1473 --
obs0.1486 39408 97.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.798→40.707 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2633 0 77 267 2977
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062959
X-RAY DIFFRACTIONf_angle_d0.8224031
X-RAY DIFFRACTIONf_dihedral_angle_d19.0651725
X-RAY DIFFRACTIONf_chiral_restr0.057419
X-RAY DIFFRACTIONf_plane_restr0.005520
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7982-1.84310.26891090.24981986X-RAY DIFFRACTION74
1.8431-1.8930.21651190.20162553X-RAY DIFFRACTION93
1.893-1.94870.21711360.17052687X-RAY DIFFRACTION98
1.9487-2.01150.18541390.15292685X-RAY DIFFRACTION100
2.0115-2.08340.17191460.14852712X-RAY DIFFRACTION100
2.0834-2.16690.17821510.14762701X-RAY DIFFRACTION100
2.1669-2.26550.17991540.14042721X-RAY DIFFRACTION100
2.2655-2.38490.16771350.13752737X-RAY DIFFRACTION100
2.3849-2.53430.17951530.14792727X-RAY DIFFRACTION100
2.5343-2.72990.16791590.14852743X-RAY DIFFRACTION100
2.7299-3.00460.17841210.14852750X-RAY DIFFRACTION100
3.0046-3.43910.15661410.14272779X-RAY DIFFRACTION100
3.4391-4.33220.14481550.12522778X-RAY DIFFRACTION100
4.3322-40.71720.17441540.14952877X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8085-0.150.13291.14790.21561.4301-0.0295-0.1382-0.05170.12330.01680.0189-0.0002-0.06310.01310.07580.0452-0.00850.0980.00280.108421.199636.421112.3004
20.4309-0.04680.39780.81090.29061.02220.0167-0.0981-0.10030.16380.05370.08170.1858-0.124-0.06420.14950.02890.00290.12460.0340.18321.434724.096917.3075
31.69740.42040.86442.82980.02281.7347-0.0665-0.14230.04880.28860.0831-0.1730.010.11760.0070.1650.0776-0.02430.1465-0.04620.106928.282540.845328.4881
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid -3:122)
2X-RAY DIFFRACTION2(chain A and resid 123:273)
3X-RAY DIFFRACTION3(chain A and resid 274:357)

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