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- PDB-9gjx: Bacillus licheniformis nitroreductase -

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Basic information

Entry
Database: PDB / ID: 9gjx
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
5-(AZIRIDIN-1-YL)-2,4-DINITROBENZAMIDE / FLAVIN MONONUCLEOTIDE / DI(HYDROXYETHYL)ETHER / NADH-dependent nitro/flavin oxidoreductase
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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)177,97054
Polymers171,0926
Non-polymers6,87848
Water6,720373
1
A: NADH-dependent nitro/flavin oxidoreductase
B: NADH-dependent nitro/flavin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,71722
Polymers57,0312
Non-polymers2,68620
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14140 Å2
ΔGint-34 kcal/mol
Surface area17900 Å2
MethodPISA
2
C: NADH-dependent nitro/flavin oxidoreductase
D: NADH-dependent nitro/flavin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,30317
Polymers57,0312
Non-polymers2,27215
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13180 Å2
ΔGint-38 kcal/mol
Surface area18520 Å2
MethodPISA
3
E: NADH-dependent nitro/flavin oxidoreductase
F: NADH-dependent nitro/flavin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,95015
Polymers57,0312
Non-polymers1,92013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12140 Å2
ΔGint-22 kcal/mol
Surface area18040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.776, 115.807, 103.807
Angle α, β, γ (deg.)90.00, 110.29, 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 , 7 types, 421 molecules

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


Mass: 456.344 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-CB1 / 5-(AZIRIDIN-1-YL)-2,4-DINITROBENZAMIDE / CB1954 / Tretazicar


Mass: 252.184 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C9H8N4O5
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 54.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 13% PEG4K, 0.1M sodium acetate pH 4.6, 0.2M ammonium sulphate, 1mM FMN. Crystals were soaked for 30 minutes in a mixture of well solution and 5% 100mM CB1954 dissolved in DMSO

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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: Jan 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→19.86 Å / Num. obs: 66476 / % possible obs: 99.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 42.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.039 / Rrim(I) all: 0.102 / Χ2: 0.92 / Net I/σ(I): 12.1
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.849 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4455 / CC1/2: 0.824 / Rpim(I) all: 0.35 / Rrim(I) all: 0.919 / Χ2: 0.86

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
DIALSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→19.86 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2193 3258 4.92 %
Rwork0.1614 --
obs0.1642 66281 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11072 0 458 373 11903
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111871
X-RAY DIFFRACTIONf_angle_d1.0715982
X-RAY DIFFRACTIONf_dihedral_angle_d8.8414469
X-RAY DIFFRACTIONf_chiral_restr0.0461643
X-RAY DIFFRACTIONf_plane_restr0.0142074
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.440.3091340.23512707X-RAY DIFFRACTION99
2.44-2.470.26341470.22332718X-RAY DIFFRACTION99
2.47-2.510.32981490.21912719X-RAY DIFFRACTION100
2.51-2.560.36061290.22122725X-RAY DIFFRACTION99
2.56-2.60.30051270.21792705X-RAY DIFFRACTION99
2.6-2.650.2981390.20932774X-RAY DIFFRACTION100
2.65-2.710.26781310.20052719X-RAY DIFFRACTION99
2.71-2.770.28091340.19722736X-RAY DIFFRACTION100
2.77-2.830.27911510.18472748X-RAY DIFFRACTION100
2.83-2.90.2481290.18942705X-RAY DIFFRACTION100
2.9-2.980.27531480.18862712X-RAY DIFFRACTION100
2.98-3.070.2541440.18472749X-RAY DIFFRACTION100
3.07-3.170.27331620.17642707X-RAY DIFFRACTION100
3.17-3.280.2121310.15932727X-RAY DIFFRACTION100
3.28-3.410.22641570.162751X-RAY DIFFRACTION100
3.41-3.560.19421350.15682772X-RAY DIFFRACTION100
3.56-3.750.20171570.14832726X-RAY DIFFRACTION100
3.75-3.980.20111490.14822752X-RAY DIFFRACTION100
3.98-4.290.18631370.13182753X-RAY DIFFRACTION100
4.29-4.710.17721320.12132770X-RAY DIFFRACTION100
4.71-5.380.1851500.13292749X-RAY DIFFRACTION100
5.38-6.740.2161660.16512751X-RAY DIFFRACTION100
6.74-19.860.17511200.16062848X-RAY DIFFRACTION100

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