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- PDB-7nmp: E. coli NfsA with hydroquinone -

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Basic information

Entry
Database: PDB / ID: 7nmp
TitleE. coli NfsA with hydroquinone
ComponentsOxygen-insensitive NADPH nitroreductase
KeywordsOXIDOREDUCTASE / complex with quinone product / 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 / Oxygen-insensitive NADPH nitroreductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsDay, M.D. / Jarrom, D. / 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
DepositionFeb 23, 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

Downloads & links

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Assembly

Deposited unit
A: Oxygen-insensitive NADPH nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6998
Polymers26,8331
Non-polymers8667
Water5,170287
1
A: Oxygen-insensitive NADPH nitroreductase
hetero molecules

A: Oxygen-insensitive NADPH nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,39816
Polymers53,6652
Non-polymers1,73214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area13740 Å2
ΔGint-93 kcal/mol
Surface area18260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.985, 52.022, 64.770
Angle α, β, γ (deg.)90.000, 134.160, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-617-

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
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

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Non-polymers , 6 types, 294 molecules

#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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / 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-HQE / benzene-1,4-diol


Mass: 110.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.07 Å3/Da / Density % sol: 40.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 28% PEG 3,000; 100 mM imidazole pH 7.0; 20% DMSO,25 mM hydroxyquinone

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 291 / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: May 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.25→46.46 Å / Num. obs: 59285 / % possible obs: 97.6 % / Redundancy: 6.39 % / Rsym value: 0.05 / Net I/σ(I): 19.2
Reflection shellResolution: 1.25→1.35 Å / Mean I/σ(I) obs: 2.4 / Num. unique obs: 25991 / Rsym value: 0.54 / % possible all: 84.9

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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: 1.25→46.03 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.533 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY SEQRES 1 A 240 MET THR PRO THR ILE GLU LEU ILE CYS GLY HIS ARG SER
RfactorNum. reflection% reflectionSelection details
Rfree0.1549 2974 5 %RANDOM
Rwork0.1232 ---
obs0.1248 56273 97.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.66 Å2 / Biso mean: 16.149 Å2 / Biso min: 6.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å2-0 Å20.17 Å2
2---1.08 Å2-0 Å2
3---0.37 Å2
Refinement stepCycle: final / Resolution: 1.25→46.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1875 0 68 298 2241
Biso mean--17.03 30.14 -
Num. residues----240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0172171
X-RAY DIFFRACTIONr_bond_other_d0.0010.0192061
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.8712968
X-RAY DIFFRACTIONr_angle_other_deg1.1972.6614751
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8295281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77322.261115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.31515364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0261516
X-RAY DIFFRACTIONr_chiral_restr0.1010.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022549
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_restr1.79934230
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.25→1.283 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 154 -
Rwork0.262 3133 -
all-3287 -
obs--73.47 %

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