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- PDB-5hei: Structure of B. megaterium NfrA2 -

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Basic information

Entry
Database: PDB / ID: 5hei
TitleStructure of B. megaterium NfrA2
ComponentsNfrA2
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 / NADPH-dependent oxidoreductase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 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 6, 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: NfrA2
B: NfrA2
C: NfrA2
D: NfrA2
E: NfrA2
F: NfrA2
G: NfrA2
H: NfrA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,14023
Polymers224,7738
Non-polymers4,36715
Water4,468248
1
A: NfrA2
B: NfrA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1064
Polymers56,1932
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12400 Å2
ΔGint-75 kcal/mol
Surface area18690 Å2
MethodPISA
2
C: NfrA2
D: NfrA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5128
Polymers56,1932
Non-polymers1,3196
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13330 Å2
ΔGint-122 kcal/mol
Surface area18160 Å2
MethodPISA
3
E: NfrA2
F: NfrA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1064
Polymers56,1932
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12350 Å2
ΔGint-67 kcal/mol
Surface area18530 Å2
MethodPISA
4
G: NfrA2
H: NfrA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4167
Polymers56,1932
Non-polymers1,2235
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13280 Å2
ΔGint-123 kcal/mol
Surface area18080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.440, 158.190, 103.860
Angle α, β, γ (deg.)90.00, 102.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
NfrA2


Mass: 28096.627 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: Histidine Tag (expression Tag): residue 248 to 253 / Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: nfrA2 / Plasmid: pEXP5-CT/TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): Star pLysS / References: UniProt: A0A0K0VJM8
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.19 Å3/Da / Density % sol: 43.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: Ammonium Sulfate, Mes pH6.5, MPD / PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97942 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2.84→50 Å / Num. all: 45685 / Num. obs: 44446 / % possible obs: 97.3 % / Redundancy: 2.9 % / Biso Wilson estimate: 58.6 Å2 / Rsym value: 0.245 / Net I/σ(I): 4.88
Reflection shellResolution: 2.84→3.01 Å / Redundancy: 2.84 % / Mean I/σ(I) obs: 1.21 / % possible all: 92.6

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZCH

1zch


Resolution: 2.84→28.63 Å / Cor.coef. Fo:Fc: 0.9054 / Cor.coef. Fo:Fc free: 0.847 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.407
RfactorNum. reflection% reflectionSelection details
Rfree0.2472 2220 5 %RANDOM
Rwork0.2027 ---
obs0.2049 44407 97.18 %-
Displacement parametersBiso mean: 59.86 Å2
Baniso -1Baniso -2Baniso -3
1--7.2767 Å20 Å21.1346 Å2
2--7.7006 Å20 Å2
3----0.4239 Å2
Refine analyzeLuzzati coordinate error obs: 0.45 Å
Refinement stepCycle: 1 / Resolution: 2.84→28.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15296 0 289 248 15833
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00815866HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0521528HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5576SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes448HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2447HARMONIC5
X-RAY DIFFRACTIONt_it15866HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.04
X-RAY DIFFRACTIONt_other_torsion21.58
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2121SEMIHARMONIC5
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_contact18355SEMIHARMONIC4
LS refinement shellResolution: 2.84→2.91 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3352 143 4.98 %
Rwork0.2368 2731 -
all0.2416 2874 -
obs--97.18 %
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)
12.00110.34540.05942.5384-0.06291.94210.03970.0790.04210.0691-0.1146-0.20070.03040.19480.0749-0.6089-0.00510.0457-0.5562-0.03910.463813.3323-10.529699.6074
21.70950.43380.16981.5057-0.72251.3455-0.0038-0.1498-0.03540.2007-0.04110.0581-0.0589-0.15790.0449-0.41820.01340.0221-0.3959-0.02840.4736-1.4568-12.101104.8794
31.9311-0.44140.10272.71890.01521.16470.1699-0.0589-0.2880.0781-0.06410.2692-0.0953-0.1694-0.1058-0.56180.02610.047-0.4455-0.00660.5474-17.0834-27.340453.24
41.0035-0.0979-0.37392.1859-0.21981.21420.09950.0889-0.1739-0.1865-0.0767-0.1031-0.17560.2402-0.0228-0.530.037-0.0071-0.43530.01870.5222-2.2852-28.931347.9998
52.7130.9356-0.51963.47190.82091.47830.14490.07670.17830.1099-0.21750.47080.124-0.31910.0726-0.27640.0028-0.0074-0.1975-0.02540.648-28.3226-53.457899.736
61.89410.31080.29982.42380.06721.55380.108-0.16660.00990.2255-0.1436-0.11630.09750.16970.0356-0.2224-0.0328-0.0325-0.2541-0.00490.5628-13.5342-51.8434104.9957
71.3911-0.4624-0.43072.02840.02281.44560.1546-0.08160.31580.0382-0.1233-0.3277-0.05720.1613-0.0313-0.51760.00890.0116-0.44020.07720.582724.8969-70.322653.1741
80.9526-0.34920.04892.3721-0.16731.35620.11120.0960.0209-0.2872-0.17250.12550.0761-0.1870.0614-0.51210.0176-0.0185-0.4171-0.00730.502810.1213-68.720247.8742
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }

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