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- PDB-8qq7: Structure of SpNOX: a Bacterial NADPH oxidase -

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Basic information

Entry
Database: PDB / ID: 8qq7
TitleStructure of SpNOX: a Bacterial NADPH oxidase
ComponentsFAD-binding FR-type domain-containing protein
KeywordsELECTRON TRANSPORT / NADPH oxidase / Reactive Oxygen Species production / membrane protein / Streptococcus pneumoniae / F397W mutant / electron transport.
Function / homology
Function and homology information


2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / oxidoreductase activity / membrane / metal ion binding
Similarity search - Function
: / FAD-binding 8 / FAD-binding domain / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel
Similarity search - Domain/homology
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / PROTOPORPHYRIN IX CONTAINING FE / FAD-binding FR-type domain-containing protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.62 Å
AuthorsThepaut, M. / Petit-Hartlein, I. / Vermot, A. / Chaptal, V. / Humm, A.S. / Dupeux, F. / Marquez, J.A. / Smith, S. / Fieschi, F.
Funding support France, European Union, 3items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-17-CE11-0013 France
Other governmentEmergence program from Universite Grenoble Alpes
iNEXT-Discovery871037European Union
CitationJournal: Elife / Year: 2024
Title: X-ray structure and enzymatic study of a bacterial NADPH oxidase highlight the activation mechanism of eukaryotic NOX.
Authors: Petit-Hartlein, I. / Vermot, A. / Thepaut, M. / Humm, A.S. / Dupeux, F. / Dupuy, J. / Chaptal, V. / Marquez, J.A. / Smith, S.M.E. / Fieschi, F.
History
DepositionOct 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FAD-binding FR-type domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2514
Polymers46,2311
Non-polymers2,0213
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-53 kcal/mol
Surface area20950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.967, 145.967, 153.619
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein FAD-binding FR-type domain-containing protein


Mass: 46230.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: spr0531 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8CZ28
#2: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H35N9O15P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 5.11 Å3/Da / Density % sol: 75.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Protein: 4.04 mg/ml in 50 mM Tris pH 7, 300 mM NaCl, 0.025 mM MNG3, 0.01 mM FAD. Crystallization condition: 30.5% PEG 300, 0.15 M Li2SO4, 0.15 M NaCl and 0.1 M MES pH6. Drop: 6 uL of protein + 6 uL of well.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 3.62→47.82 Å / Num. obs: 5508 / % possible obs: 90.9 % / Redundancy: 20 % / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.017 / Rrim(I) all: 0.074 / Net I/σ(I): 19.6
Reflection shellResolution: 3.62→3.95 Å / Redundancy: 20 % / Rmerge(I) obs: 2 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 275 / Rpim(I) all: 0.465 / % possible all: 85.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
STARANISOdata scaling
PHASERphasing
Cootmodel building
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: model from PROMALS3D and I-TASSER

Resolution: 3.62→47.82 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.905 / SU B: 78.364 / SU ML: 1.08 / Cross valid method: THROUGHOUT / ESU R Free: 1.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.32003 245 4.4 %RANDOM
Rwork0.26152 ---
obs0.2642 5262 47.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.6 Å / Solvent model: MASK
Displacement parametersBiso mean: 201.602 Å2
Baniso -1Baniso -2Baniso -3
1-1.73 Å20.86 Å20 Å2
2--1.73 Å2-0 Å2
3----5.61 Å2
Refinement stepCycle: 1 / Resolution: 3.62→47.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3404 0 0 0 3404
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0123520
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7271.6694805
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4165398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.37822.025163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.80315573
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2451513
X-RAY DIFFRACTIONr_chiral_restr0.1350.2437
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022660
X-RAY DIFFRACTIONr_gen_planes_other
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_it19.41518.6981595
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it31.66428.0011992
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it23.46221.0851922
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.623→3.717 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.507 3 -
Rwork0.36 54 -
obs--6.82 %

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