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- PDB-9c0w: AzrC from Bacillus pacificus ROC1 bound to malachite green -

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Basic information

Entry
Database: PDB / ID: 9c0w
TitleAzrC from Bacillus pacificus ROC1 bound to malachite green
ComponentsFMN-dependent NADH:quinone oxidoreductase 3
KeywordsFLAVOPROTEIN / Azoreductase / FMN / Malachite green
Function / homology
Function and homology information


FMN-dependent NADH-azoreductase / Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor / oxidoreductase activity, acting on NAD(P)H as acceptor / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / FMN binding / electron transfer activity
Similarity search - Function
NADH:quinone oxidoreductase, FMN-dependent / : / Flavodoxin-like fold / Flavodoxin-like fold / Flavoprotein-like superfamily
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / MALACHITE GREEN / FMN-dependent NADH:quinone oxidoreductase 3
Similarity search - Component
Biological speciesBacillus pacificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsBreeze, C.W. / Jackson, C.J. / Frkic, R.L.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: Sci Rep / Year: 2025
Title: Isolation, identification, and characterisation of the malachite green detoxifying bacterial strain Bacillus pacificus ROC1 and the azoreductase AzrC.
Authors: Bibi, S. / Breeze, C.W. / Jadoon, V. / Fareed, A. / Syed, A. / Frkic, R.L. / Zaffar, H. / Ali, M. / Zeb, I. / Jackson, C.J. / Naqvi, T.A.
History
DepositionMay 28, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2025Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FMN-dependent NADH:quinone oxidoreductase 3
B: FMN-dependent NADH:quinone oxidoreductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7695
Polymers50,5272
Non-polymers1,2423
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-30 kcal/mol
Surface area20660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.133, 74.164, 135.543
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 FMN-dependent NADH:quinone oxidoreductase 3 / Azo-dye reductase 3 / FMN-dependent NADH-azo compound oxidoreductase 3 / FMN-dependent NADH-azoreductase 3


Mass: 25263.291 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus pacificus (bacteria) / Gene: azoR3, BCE_2269 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q738X4, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor, FMN-dependent NADH-azoreductase
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-MGR / MALACHITE GREEN


Mass: 329.458 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H25N2 / Feature type: SUBJECT OF INVESTIGATION / Comment: Antimicrobial*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O
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: 2.34 Å3/Da / Density % sol: 47.53 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M sodium acetate, 0.1 M bis-tris pH 5.5, 20% (w/v) PEG 10K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 28, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.35→39.78 Å / Num. obs: 20498 / % possible obs: 99.9 % / Redundancy: 12.2 % / CC1/2: 0.992 / Rmerge(I) obs: 0.29 / Rpim(I) all: 0.088 / Rrim(I) all: 0.304 / Χ2: 1.03 / Net I/σ(I): 9.2 / Num. measured all: 249608
Reflection shellResolution: 2.35→2.43 Å / % possible obs: 100 % / Redundancy: 12.7 % / Rmerge(I) obs: 1.643 / Num. measured all: 24816 / Num. unique obs: 1960 / CC1/2: 0.937 / Rpim(I) all: 0.476 / Rrim(I) all: 1.711 / Χ2: 0.88 / Net I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→39.78 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 34.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2841 1039 5.13 %
Rwork0.2245 --
obs0.2276 20237 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→39.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3351 0 87 173 3611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001
X-RAY DIFFRACTIONf_angle_d0.346
X-RAY DIFFRACTIONf_dihedral_angle_d11.151224
X-RAY DIFFRACTIONf_chiral_restr0.038512
X-RAY DIFFRACTIONf_plane_restr0.003619
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.470.39361370.30352717X-RAY DIFFRACTION99
2.47-2.630.33651430.27922690X-RAY DIFFRACTION99
2.63-2.830.34281410.2722724X-RAY DIFFRACTION99
2.83-3.120.30811530.24892732X-RAY DIFFRACTION100
3.12-3.570.33251460.2382744X-RAY DIFFRACTION99
3.57-4.490.26461550.21142665X-RAY DIFFRACTION96
4.49-39.780.22551640.18332926X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 8.1516 Å / Origin y: -2.8985 Å / Origin z: -16.2444 Å
111213212223313233
T0.1599 Å20.0028 Å2-0.0129 Å2-0.676 Å20.1504 Å2--0.4693 Å2
L2.1278 °20.1297 °20.3036 °2-1.0291 °20.0753 °2--0.5149 °2
S0.0276 Å °0.4352 Å °0.1976 Å °-0.1231 Å °0.0149 Å °0.0686 Å °-0.0219 Å °0.0436 Å °-0.0118 Å °
Refinement TLS groupSelection details: all

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