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- PDB-9gjy: Bacillus licheniformis nitroreductase -

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Basic information

Entry
Database: PDB / ID: 9gjy
TitleBacillus licheniformis nitroreductase
ComponentsNADH-dependent nitro/flavin oxidoreductase
KeywordsOXIDOREDUCTASE / nitroreductase / prodrug activation / NAD(P)H-dependent oxidoreductase
Function / homology
Function and homology information


oxidoreductase activity, acting on other nitrogenous compounds as donors, with NAD or NADP as acceptor / 2,4,6-trinitrotoluene catabolic process / cytosol
Similarity search - Function
Oxygen-insensitive NAD(P)H nitroreductase NfsB-like / : / Nitroreductase / Nitroreductase family / Nitroreductase-like
Similarity search - Domain/homology
ACETATE ION / FLAVIN MONONUCLEOTIDE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / NADH-dependent nitro/flavin oxidoreductase
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsCrennell, S.J. / Danson, M.J. / Emptage, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of Bacillus licheniformis nitroreductase and analysis of prodrug specificity
Authors: Crennell, S.J. / Danson, M.J. / Emptage, C. / Nesbitt, E. / Porter, M.
History
DepositionAug 23, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADH-dependent nitro/flavin oxidoreductase
B: NADH-dependent nitro/flavin oxidoreductase
C: NADH-dependent nitro/flavin oxidoreductase
D: NADH-dependent nitro/flavin oxidoreductase
E: NADH-dependent nitro/flavin oxidoreductase
F: NADH-dependent nitro/flavin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,95238
Polymers171,0926
Non-polymers4,85932
Water20,2671125
1
A: NADH-dependent nitro/flavin oxidoreductase
B: NADH-dependent nitro/flavin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,83716
Polymers57,0312
Non-polymers1,80714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12470 Å2
ΔGint-26 kcal/mol
Surface area18880 Å2
MethodPISA
2
C: NADH-dependent nitro/flavin oxidoreductase
D: NADH-dependent nitro/flavin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,41410
Polymers57,0312
Non-polymers1,3838
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11200 Å2
ΔGint-42 kcal/mol
Surface area19210 Å2
MethodPISA
3
E: NADH-dependent nitro/flavin oxidoreductase
F: NADH-dependent nitro/flavin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,70012
Polymers57,0312
Non-polymers1,66910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11410 Å2
ΔGint-38 kcal/mol
Surface area18050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.106, 115.380, 103.228
Angle α, β, γ (deg.)90.00, 109.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
NADH-dependent nitro/flavin oxidoreductase


Mass: 28515.387 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: CAMR culture collection / Source: (gene. exp.) Bacillus licheniformis (bacteria) / Gene: nfsB, BL03079 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q65MG6

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Non-polymers , 8 types, 1157 molecules

#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1125 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.69 Å3/Da / Density % sol: 54.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 13% PEG 4K, 0.1M sodium acetate pH 4.6, 0.2M ammonium sulphate, 1mM FMN

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.62→60.33 Å / Num. obs: 209349 / % possible obs: 97.5 % / Redundancy: 28.5 % / Biso Wilson estimate: 21.77 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.015 / Rrim(I) all: 0.082 / Χ2: 0.87 / Net I/σ(I): 24.1
Reflection shellResolution: 1.62→1.65 Å / Redundancy: 29.1 % / Rmerge(I) obs: 1.611 / Mean I/σ(I) obs: 2 / Num. unique obs: 10265 / CC1/2: 0.927 / Rpim(I) all: 0.303 / Rrim(I) all: 1.64 / Χ2: 0.68 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
DIALSdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→57.69 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2059 10279 4.92 %
Rwork0.1734 --
obs0.1749 208979 97.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.62→57.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11195 0 324 1125 12644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111913
X-RAY DIFFRACTIONf_angle_d1.1116037
X-RAY DIFFRACTIONf_dihedral_angle_d9.2384523
X-RAY DIFFRACTIONf_chiral_restr0.0541657
X-RAY DIFFRACTIONf_plane_restr0.0242091
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.640.35313470.33776476X-RAY DIFFRACTION95
1.64-1.660.35813560.32066405X-RAY DIFFRACTION95
1.66-1.680.32483580.29886549X-RAY DIFFRACTION96
1.68-1.70.32473570.28136421X-RAY DIFFRACTION95
1.7-1.720.29253520.26326546X-RAY DIFFRACTION96
1.72-1.750.29283430.24826446X-RAY DIFFRACTION96
1.75-1.770.28133350.24556494X-RAY DIFFRACTION96
1.77-1.80.27333490.23776608X-RAY DIFFRACTION96
1.8-1.820.2713590.22846499X-RAY DIFFRACTION96
1.82-1.850.25933770.22256514X-RAY DIFFRACTION96
1.85-1.890.24873320.2246599X-RAY DIFFRACTION97
1.89-1.920.27553360.23246555X-RAY DIFFRACTION97
1.92-1.960.26523450.2276573X-RAY DIFFRACTION97
1.96-20.26883370.21736581X-RAY DIFFRACTION97
2-2.040.25233330.20626629X-RAY DIFFRACTION97
2.04-2.090.23713130.20236631X-RAY DIFFRACTION97
2.09-2.140.21063230.18986667X-RAY DIFFRACTION97
2.14-2.20.23223280.18426626X-RAY DIFFRACTION98
2.2-2.260.2253010.18096704X-RAY DIFFRACTION98
2.26-2.340.2153460.18066645X-RAY DIFFRACTION98
2.34-2.420.21523490.17936645X-RAY DIFFRACTION98
2.42-2.520.20253430.16946741X-RAY DIFFRACTION98
2.52-2.630.20783440.16766662X-RAY DIFFRACTION98
2.63-2.770.19583270.16296734X-RAY DIFFRACTION98
2.77-2.940.18543760.16276707X-RAY DIFFRACTION99
2.94-3.170.21053550.16236706X-RAY DIFFRACTION99
3.17-3.490.17973300.14726802X-RAY DIFFRACTION99
3.49-3.990.16963390.14186793X-RAY DIFFRACTION99
3.99-5.030.13053520.11916822X-RAY DIFFRACTION99
5.03-57.690.20783370.17576920X-RAY DIFFRACTION99

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