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- PDB-5hdj: Structure of B. megaterium NfrA1 -

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Basic information

Entry
Database: PDB / ID: 5hdj
TitleStructure of B. megaterium NfrA1
ComponentsNfrA1
KeywordsOXIDOREDUCTASE / Nitroreductase enzyme / dimer
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
Flavin oxidoreductase Frp family / NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / NfrA1
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsVigouroux, A. / Morera, S.
CitationJournal: Biochem.J. / Year: 2016
Title: Functional and structural characterization of two Bacillus megaterium nitroreductases biotransforming the herbicide mesotrione.
Authors: Carles, L. / Besse-Hoggan, P. / Joly, M. / Vigouroux, A. / Morera, S. / Batisson, I.
History
DepositionJan 5, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Jan 10, 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: NfrA1
B: NfrA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7917
Polymers58,6922
Non-polymers1,0995
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12710 Å2
ΔGint-83 kcal/mol
Surface area18920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.390, 86.870, 92.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NfrA1


Mass: 29346.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: FMN / Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: nfrA1 / Plasmid: pEXP5-CT/TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): Star pLysS / References: UniProt: A0A0K0VJM9
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 4000, Mes pH6.5 / PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.89→48 Å / Num. all: 36958 / Num. obs: 36741 / % possible obs: 99.4 % / Redundancy: 6.9 % / Biso Wilson estimate: 23.59 Å2 / Rsym value: 0.0218 / Net I/σ(I): 7.52
Reflection shellResolution: 1.89→2.01 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 1.65 / % possible all: 96.4

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
PHASERphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N2S

3n2s


Resolution: 1.89→36.26 Å / Cor.coef. Fo:Fc: 0.9503 / Cor.coef. Fo:Fc free: 0.9308 / SU R Cruickshank DPI: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.162 / SU Rfree Blow DPI: 0.135 / SU Rfree Cruickshank DPI: 0.133
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1836 5 %RANDOM
Rwork0.1743 ---
obs0.1759 36733 99.01 %-
Displacement parametersBiso mean: 24.31 Å2
Baniso -1Baniso -2Baniso -3
1-2.5347 Å20 Å20 Å2
2---1.6417 Å20 Å2
3----0.8929 Å2
Refine analyzeLuzzati coordinate error obs: 0.204 Å
Refinement stepCycle: 1 / Resolution: 1.89→36.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3957 0 74 276 4307
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014112HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.035554HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1467SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes118HARMONIC2
X-RAY DIFFRACTIONt_gen_planes628HARMONIC5
X-RAY DIFFRACTIONt_it4112HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.46
X-RAY DIFFRACTIONt_other_torsion18.21
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion538SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5125SEMIHARMONIC4
LS refinement shellResolution: 1.89→1.95 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2985 131 4.97 %
Rwork0.2622 2506 -
all0.2641 2637 -
obs--99.01 %
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)
10.3523-0.0844-0.02310.2364-0.0010.33370.00980.0034-0.01150.0097-0.00450.05350.0304-0.01-0.0053-0.1438-0.0088-0.0028-0.06760.002-0.114556.378691.8379.9102
20.58350.0645-0.1240.48490.02210.21040.0271-0.03610.01530.0512-0.0121-0.0147-0.00750.062-0.0149-0.1243-0.0028-0.0113-0.03350.0024-0.129170.195697.174815.9315
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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