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- PDB-7nb9: E. coli NfsA with nitrofurantoin -

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Basic information

Entry
Database: PDB / ID: 7nb9
TitleE. coli NfsA with nitrofurantoin
ComponentsOxygen-insensitive NADPH nitroreductase
KeywordsOXIDOREDUCTASE / complex with Antibiotic substrate / flavoprotein / nitroreductase
Function / homology
Function and homology information


NAD(P)H dehydrogenase (quinone) activity / Oxidoreductases / FMN binding / protein homodimerization activity / cytosol
Similarity search - Function
Flavin oxidoreductase Frp family / Nitroreductase / Nitroreductase family / Nitroreductase-like
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Chem-U6Z / Oxygen-insensitive NADPH nitroreductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å
AuthorsDay, M.D. / Jarrom, D. / Grainger, A.I. / Parr, R.J. / Hyde, E.I. / White, S.A.
CitationJournal: Biochem.J. / Year: 2021
Title: The structures of E. coli NfsA bound to the antibiotic nitrofurantoin; to 1,4-benzoquinone and to FMN.
Authors: Day, M.A. / Jarrom, D. / Christofferson, A.J. / Graziano, A.E. / Anderson, J.L.R. / Searle, P.F. / Hyde, E.I. / White, S.A.
History
DepositionJan 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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

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Assembly

Deposited unit
A: Oxygen-insensitive NADPH nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6054
Polymers26,8331
Non-polymers7733
Water5,350297
1
A: Oxygen-insensitive NADPH nitroreductase
hetero molecules

A: Oxygen-insensitive NADPH nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2118
Polymers53,6652
Non-polymers1,5456
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area12680 Å2
ΔGint-79 kcal/mol
Surface area18400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.396, 51.857, 64.583
Angle α, β, γ (deg.)90.000, 134.100, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-628-

HOH

21A-693-

HOH

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Components

#1: Protein Oxygen-insensitive NADPH nitroreductase / Modulator of drug activity A


Mass: 26832.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: nfsA, mda18, mdaA, ybjB, b0851, JW0835 / Plasmid: pPS1341A1 / Details (production host): pET24 derivative / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P17117, Oxidoreductases
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-U6Z / 1-[(~{E})-(5-nitrofuran-2-yl)methylideneamino]imidazolidine-2,4-dione / Nitrofurantoin


Mass: 238.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H6N4O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.05 Å3/Da / Density % sol: 39.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM imidazole pH 7, 20-26 % PEG 3,000, 3.5 mM nitrofurantoin, 20% DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.09→45.69 Å / Num. obs: 83276 / % possible obs: 91.4 % / Redundancy: 3.4 % / Rsym value: 0.037 / Net I/σ(I): 19.4
Reflection shellResolution: 1.09→1.15 Å / Redundancy: 2.33 % / Mean I/σ(I) obs: 3.69 / Num. unique obs: 9425 / Rsym value: 0.22 / % possible all: 64.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F5V

1f5v


Resolution: 1.09→45.69 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.837 / SU ML: 0.018 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.024 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1255 4153 5 %RANDOM
Rwork0.1043 ---
obs0.1054 79095 92.22 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 177.45 Å2 / Biso mean: 16.984 Å2 / Biso min: 7.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20.59 Å2
2---2.07 Å20 Å2
3---0.21 Å2
Refinement stepCycle: final / Resolution: 1.09→45.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1887 0 52 312 2251
Biso mean--13.12 31.45 -
Num. residues----240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0142145
X-RAY DIFFRACTIONr_bond_other_d0.0030.0171902
X-RAY DIFFRACTIONr_angle_refined_deg1.8391.6852948
X-RAY DIFFRACTIONr_angle_other_deg1.1751.6474482
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1675277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.89121.583120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.05915363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6821519
X-RAY DIFFRACTIONr_chiral_restr0.1040.2281
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.022500
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02386
X-RAY DIFFRACTIONr_rigid_bond_restr6.08134045
X-RAY DIFFRACTIONr_sphericity_free31.4315204
X-RAY DIFFRACTIONr_sphericity_bonded17.65254115
LS refinement shellResolution: 1.09→1.119 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.211 157 -
Rwork0.179 3497 -
all-3654 -
obs--54.68 %

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