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- PDB-7niy: E. coli NfsA with FMN -

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Basic information

Entry
Database: PDB / ID: 7niy
TitleE. coli NfsA with FMN
ComponentsOxygen-insensitive NADPH nitroreductase
KeywordsOXIDOREDUCTASE / complex with inhibitor FMN / 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 / IMIDAZOLE / Oxygen-insensitive NADPH nitroreductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.03 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 14, 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 1.2Nov 6, 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

Downloads & links

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Assembly

Deposited unit
A: Oxygen-insensitive NADPH nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,26310
Polymers26,8331
Non-polymers1,4319
Water5,314295
1
A: Oxygen-insensitive NADPH nitroreductase
hetero molecules

A: Oxygen-insensitive NADPH nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,52720
Polymers53,6652
Non-polymers2,86118
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area15200 Å2
ΔGint-78 kcal/mol
Surface area17910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.911, 52.003, 64.695
Angle α, β, γ (deg.)90.000, 133.780, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-613-

HOH

21A-688-

HOH

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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 / Mutation: C9(8QC), C90(8QC)
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 / Variant: DH5alpha / Plasmid: pPS1341A1 / Details (production host): pET24c derivative / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P17117, Oxidoreductases

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Non-polymers , 6 types, 304 molecules

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


Mass: 110.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6O2
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.03 Å3/Da / Density % sol: 39.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 30 % PEG 3,350; 100 mM Imidazole, 20 mM Hydroquinone, 15 % Ethylene Glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.03→32.36 Å / Num. obs: 99892 / % possible obs: 96.72 % / Redundancy: 8 % / Rsym value: 0.04 / Net I/σ(I): 27.89
Reflection shellResolution: 1.03→1.056 Å / Num. unique obs: 7069 / Rsym value: 0.58 / % possible all: 92.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FV5

1fv5


Resolution: 1.03→32.36 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.982 / SU B: 0.527 / SU ML: 0.012 / Cross valid method: THROUGHOUT / ESU R: 0.021 / ESU R Free: 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1183 5332 5.1 %RANDOM
Rwork0.1049 ---
obs0.1056 99892 96.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 62.52 Å2 / Biso mean: 10.377 Å2 / Biso min: 2.98 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0.08 Å2
2--0.44 Å20 Å2
3----0.1 Å2
Refinement stepCycle: final / Resolution: 1.03→32.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1903 0 81 318 2302
Biso mean--10.79 24.96 -
Num. residues----240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0182403
X-RAY DIFFRACTIONr_bond_other_d0.0020.022201
X-RAY DIFFRACTIONr_angle_refined_deg1.7521.8913292
X-RAY DIFFRACTIONr_angle_other_deg1.2462.8985119
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.115304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.92923.739115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.315404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8211522
X-RAY DIFFRACTIONr_chiral_restr0.0960.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022780
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02506
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_restr2.12234603
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.03→1.056 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.253 360 -
Rwork0.232 7069 -
obs--92.3 %

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