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- PDB-6qu0: Structure of azoreductase from Bacillus sp. A01 -

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Basic information

Entry
Database: PDB / ID: 6qu0
TitleStructure of azoreductase from Bacillus sp. A01
ComponentsFMN-dependent NADH-azoreductase
KeywordsOXIDOREDUCTASE / Flavoprotein Oxidoreductase FMN Azoreductase Azo dyes
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 / Flavodoxin domain / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / FMN dependent NADH:quinone oxidoreductase
Similarity search - Component
Biological speciesBacillus okhensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSavino, S. / Fraaije, M.W.
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Mechanistic and Crystallographic Studies of Azoreductase AzoA fromBacillus wakoensisA01.
Authors: Romero, E. / Savino, S. / Fraaije, M.W. / Loncar, N.
History
DepositionFeb 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 4, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Apr 22, 2020Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.4Jan 24, 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 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FMN-dependent NADH-azoreductase
B: FMN-dependent NADH-azoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3007
Polymers47,1072
Non-polymers1,1935
Water2,486138
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-48 kcal/mol
Surface area18130 Å2
Unit cell
Length a, b, c (Å)47.209, 92.970, 103.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein FMN-dependent NADH-azoreductase / Azo-dye reductase / FMN-dependent NADH-azo compound oxidoreductase


Mass: 23553.732 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus okhensis (bacteria) / Gene: azoR, LQ50_08590 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0B0IKH9, Oxidoreductases; Acting on other nitrogenous compounds as donors
#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48.75 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / Details: 0.15M ammonium sulfate 25% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.79→42.92 Å / Num. obs: 43095 / % possible obs: 99 % / Redundancy: 6.8 % / Net I/σ(I): 8.4
Reflection shellResolution: 1.79→1.83 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W7A

3w7a


Resolution: 1.8→42.96 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.883 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23418 2092 4.9 %RANDOM
Rwork0.2085 ---
obs0.20975 40837 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.947 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å2-0 Å2-0 Å2
2---1.77 Å20 Å2
3---2.19 Å2
Refinement stepCycle: LAST / Resolution: 1.8→42.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3313 0 79 138 3530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133501
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173162
X-RAY DIFFRACTIONr_angle_refined_deg1.6321.6644744
X-RAY DIFFRACTIONr_angle_other_deg1.3671.5947362
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2685424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81823.735166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.04915566
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.041510
X-RAY DIFFRACTIONr_chiral_restr0.0750.2441
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023860
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02718
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9853.291690
X-RAY DIFFRACTIONr_mcbond_other2.9863.2891689
X-RAY DIFFRACTIONr_mcangle_it4.2724.9212110
X-RAY DIFFRACTIONr_mcangle_other4.2714.9212111
X-RAY DIFFRACTIONr_scbond_it3.7343.7071811
X-RAY DIFFRACTIONr_scbond_other3.643.6511804
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4255.2972621
X-RAY DIFFRACTIONr_long_range_B_refined11.0862.81514756
X-RAY DIFFRACTIONr_long_range_B_other11.08462.63414658
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.797→1.844 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 129 -
Rwork0.36 2867 -
obs--95.26 %

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