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- PDB-8qq5: Structure of WT SpNox DH domain: a bacterial NADPH oxidase. -

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Basic information

Entry
Database: PDB / ID: 8qq5
TitleStructure of WT SpNox DH domain: a bacterial NADPH oxidase.
ComponentsOxidoreductase
KeywordsELECTRON TRANSPORT / NADPH oxidase / Reactive Oxygen Species production / membrane protein / Dehydrogenase domain / Streptococcus pneumoniae.
Function / homology
Function and homology information


ferredoxin-NAD+ reductase / ferredoxin-NAD+ reductase activity / membrane
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
FLAVIN-ADENINE DINUCLEOTIDE / Oxidoreductase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsThepaut, M. / Petit-Hartlein, I. / Vermot, A. / 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 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Oxidoreductase
B: Oxidoreductase
C: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5027
Polymers76,8603
Non-polymers1,6424
Water1,964109
1
A: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4413
Polymers25,6201
Non-polymers8212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6562
Polymers25,6201
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4062
Polymers25,6201
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.880, 104.880, 139.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Oxidoreductase /


Mass: 25620.119 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: ndoR / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4J2B4U9
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
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: 2.49 Å3/Da / Density % sol: 50.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Protein: 15 mg/ml in 100 mM bis-TRIS propane pH 6.5, 300 mM NaCl, 5% glycerol, 0.01 mM FAD. Crystallization condition: 35% PEG MME 500 and 0.1 M sodium citrate pH5. Drop: 100 nL of protein +100 nL 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: Sep 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.5→46.9 Å / Num. obs: 26155 / % possible obs: 100 % / Redundancy: 25.96 % / CC1/2: 0.999 / Net I/σ(I): 18.99
Reflection shellResolution: 2.5→2.6 Å / Num. unique obs: 2978 / CC1/2: 0.639

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
REFMAC5.8.0258refinement
Cootmodel building
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→46.9 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.904 / SU B: 13.557 / SU ML: 0.289 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.604 / ESU R Free: 0.34 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2896 1377 5 %RANDOM
Rwork0.1969 ---
obs0.2014 26155 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 254.04 Å2 / Biso mean: 70.243 Å2 / Biso min: 30.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.07 Å20 Å20 Å2
2---1.07 Å20 Å2
3---2.15 Å2
Refinement stepCycle: final / Resolution: 2.5→46.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5343 0 108 109 5560
Biso mean--127.49 58.67 -
Num. residues----654
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0125630
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.647620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.725656
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.56822.941306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.6615955
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2761524
X-RAY DIFFRACTIONr_chiral_restr0.1070.2712
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024378
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 99 -
Rwork0.405 1881 -
all-1980 -
obs--100 %

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