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- PDB-7nnx: E. coli NfsA with 1,4-benzoquinone -

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Basic information

Entry
Database: PDB / ID: 7nnx
TitleE. coli NfsA with 1,4-benzoquinone
ComponentsOxygen-insensitive NADPH nitroreductase
KeywordsOXIDOREDUCTASE / complex with benzoquinone 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 / benzene-1,4-diol / 1,4-benzoquinone / Oxygen-insensitive NADPH nitroreductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDay, M.D. / Jarrom, D. / 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
DepositionFeb 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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)27,8079
Polymers26,8331
Non-polymers9748
Water4,648258
1
A: Oxygen-insensitive NADPH nitroreductase
hetero molecules

A: Oxygen-insensitive NADPH nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,61418
Polymers53,6652
Non-polymers1,94916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area14300 Å2
ΔGint-79 kcal/mol
Surface area18150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.767, 51.963, 64.686
Angle α, β, γ (deg.)90.000, 133.920, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#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
Details: Cys90 has been modified by reaction with 1,4 benzoquinone to give a quinol adduct.
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

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Non-polymers , 7 types, 266 molecules

#2: Chemical ChemComp-HQE / benzene-1,4-diol


Mass: 110.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6O2
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-PLQ / 1,4-benzoquinone / cyclohexa-2,5-diene-1,4-dione / QUINONE RING OF THE PLASTOQUINONE 9


Mass: 108.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H4O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.07 Å3/Da / Density % sol: 40.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 18% PEG 3000, 100 mM Imidazole pH 7.0, 20% DMSO, 10 mM 1,4 Benzoquinone

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Aug 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→46.59 Å / Num. obs: 23824 / % possible obs: 98.2 % / Redundancy: 11.4 % / Rsym value: 0.09 / Net I/σ(I): 24.8
Reflection shellResolution: 1.7→1.79 Å / Mean I/σ(I) obs: 4.6 / Num. unique obs: 3102 / Rsym value: 0.35 / % possible all: 88.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F5V

1f5v


Resolution: 1.7→46.59 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.527 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1699 1170 4.9 %RANDOM
Rwork0.1408 ---
obs0.1423 22647 98.19 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 80.55 Å2 / Biso mean: 17.844 Å2 / Biso min: 5.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å2-0 Å20.48 Å2
2---1.99 Å20 Å2
3---0.34 Å2
Refinement stepCycle: final / Resolution: 1.7→46.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1875 0 70 258 2203
Biso mean--18.05 26.54 -
Num. residues----240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0172171
X-RAY DIFFRACTIONr_bond_other_d0.0010.0192060
X-RAY DIFFRACTIONr_angle_refined_deg1.261.8692968
X-RAY DIFFRACTIONr_angle_other_deg1.0892.6614750
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5785281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.29322.261115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.95515364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8021516
X-RAY DIFFRACTIONr_chiral_restr0.080.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022561
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02501
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 64 -
Rwork0.194 1417 -
all-1481 -
obs--83.63 %
Refinement TLS params.Method: refined / Origin x: 3.99 Å / Origin y: -25.466 Å / Origin z: 7.214 Å
111213212223313233
T0.0779 Å2-0.0053 Å2-0.0225 Å2-0.1207 Å2-0.0007 Å2--0.0084 Å2
L0.7091 °2-0.0844 °20.1476 °2-0.3334 °20.0483 °2--1.2884 °2
S-0.0353 Å °-0.097 Å °0.0218 Å °0.065 Å °0.0078 Å °-0.0199 Å °-0.1511 Å °0.0541 Å °0.0276 Å °

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