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- PDB-7f76: Crystal Structure of FMN-dependent NADPH-quinone reductase (azoR)... -

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Basic information

Entry
Database: PDB / ID: 7f76
TitleCrystal Structure of FMN-dependent NADPH-quinone reductase (azoR) from Bacillus cohnii
ComponentsFMN-dependent NADPH-quinone reductase (azoR)
KeywordsOXIDOREDUCTASE / Quinone reductase (azoR) / FMN / NADH
Function / homology
Function and homology information


FMN binding / oxidoreductase activity / cytosol
Similarity search - Function
: / NADPH-dependent FMN reductase-like / NADPH-dependent FMN reductase / Flavoprotein-like superfamily
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / ISOPROPYL ALCOHOL / FMN-dependent NADH-azoreductase
Similarity search - Component
Biological speciesBacillus cohnii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsYoneda, K. / Sakuraba, H. / Ohshima, T.
CitationJournal: J Nutr Sci Vitaminol (Tokyo) / Year: 2025
Title: Structural and Functional Characteristics of FMN-Dependent NADPH-Indigo Reductase Homolog from Bacillus cohnii.
Authors: Yoneda, K. / Sakuraba, H. / Hayashi, J. / Naruse, Y. / Araki, T. / Ohshima, T.
History
DepositionJun 28, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2May 14, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: FMN-dependent NADPH-quinone reductase (azoR)
B: FMN-dependent NADPH-quinone reductase (azoR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,00911
Polymers43,6122
Non-polymers1,3979
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-6 kcal/mol
Surface area15390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.849, 77.552, 95.495
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11B-422-

HOH

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Components

#1: Protein FMN-dependent NADPH-quinone reductase (azoR) / FMN-dependent NADH-azoreductase


Mass: 21805.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cohnii (bacteria) / Gene: azoR / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A223KLJ1
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.14 Å3/Da / Density % sol: 42.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 35% 2-propanol, 0.1 M Tris/HCl (pH 8.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. obs: 45768 / % possible obs: 98.1 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.018 / Rrim(I) all: 0.055 / Net I/σ(I): 28
Reflection shellResolution: 1.57→1.71 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.741 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1882 / Rpim(I) all: 0.343 / Rrim(I) all: 0.821 / % possible all: 86.1

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
MOLREP11.7.03phasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GFR

3gfr


Resolution: 1.57→47.79 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.697 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1909 2385 5 %RANDOM
Rwork0.1653 ---
obs0.1666 45768 90.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.73 Å2 / Biso mean: 20.541 Å2 / Biso min: 11.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0 Å20 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.57→47.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2700 0 94 266 3060
Biso mean--21.68 33.62 -
Num. residues----345
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132838
X-RAY DIFFRACTIONr_bond_other_d0.0040.0172762
X-RAY DIFFRACTIONr_angle_refined_deg1.6891.6453832
X-RAY DIFFRACTIONr_angle_other_deg1.5271.5856350
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7745343
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.95422.734139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.78815499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0181516
X-RAY DIFFRACTIONr_chiral_restr0.090.2359
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023155
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02609
LS refinement shellResolution: 1.571→1.612 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 63 -
Rwork0.396 1171 -
all-1234 -
obs--31.8 %

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