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- PDB-8qq1: SpNOX dehydrogenase domain, mutant F397W in complex with Flavin a... -

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Basic information

Entry
Database: PDB / ID: 8qq1
TitleSpNOX dehydrogenase domain, mutant F397W in complex with Flavin adenine dinucleotide (FAD)
ComponentsOxidoreductase
KeywordsMEMBRANE PROTEIN / Streptococcus pneumoniae NADPH Oxidase (spNOX) Reactive oxygen species (ROS) membrane protein electron transfer oxidative stress
Function / homology
Function and homology information


ferredoxin-NAD+ reductase / ferredoxin-NAD+ reductase activity / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 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
BROMIDE ION / FLAVIN-ADENINE DINUCLEOTIDE / Oxidoreductase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.941 Å
AuthorsHumm, A.S. / Dupeux, F. / Vermot, A. / Petit-Harleim, I. / Fieschi, F. / Marquez, J.A.
Funding support France, European Union, 3items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-17-CE11-0013 France
Other governmentEmergence Program from University 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Oxidoreductase
F: Oxidoreductase
G: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,36432
Polymers76,9293
Non-polymers4,43429
Water9,872548
1
C: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,06810
Polymers25,6431
Non-polymers1,4259
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,22812
Polymers25,6431
Non-polymers1,58511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,06810
Polymers25,6431
Non-polymers1,4259
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.622, 104.622, 142.688
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Oxidoreductase


Mass: 25643.154 Da / Num. of mol.: 3 / Mutation: F397W
Source method: isolated from a genetically manipulated source
Details: Flavin Adenin dinucleotide / Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: ndoR / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4J2B4U9
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


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


Mass: 79.904 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 548 / 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: 2.54 Å3/Da / Density % sol: 51.5 %
Description: typical crystal shape are elongated hexagon, 150 micrometr lenght 80 micrometer wide.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Crystals Obtained at the HTX Facility, EMBL Grenoble 17% w/v PEG3350, 0.1M BIS-TRIS Propane pH6.5, 0.2M Sodium bromide. Automatic harvesting and cryocooling with CrystalDirect

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 6, 2018 / Details: Vertical CRL / Horizontal elliptical mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.941→58.944 Å / Num. obs: 57719 / % possible obs: 98.4 % / Redundancy: 13.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.023 / Rrim(I) all: 0.119 / Net I/σ(I): 21.2
Reflection shellResolution: 1.941→1.974 Å / Redundancy: 12.9 % / Rmerge(I) obs: 1.829 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2772 / CC1/2: 0.723 / Rpim(I) all: 0.372 / % possible all: 95.6

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
MxCuBEdata collection
CRANK2phasing
Aimlessdata scaling
autoPROCdata processing
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.941→36.99 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.935 / SU R Cruickshank DPI: 0.157 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.168 / SU Rfree Blow DPI: 0.146 / SU Rfree Cruickshank DPI: 0.142
RfactorNum. reflection% reflectionSelection details
Rfree0.2249 2885 -RANDOM
Rwork0.1902 ---
obs0.1919 57709 97.6 %-
Displacement parametersBiso mean: 38.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.3933 Å20 Å20 Å2
2---0.3933 Å20 Å2
3---0.7865 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.941→36.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5304 0 185 548 6037
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085629HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.917637HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1922SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1050HARMONIC5
X-RAY DIFFRACTIONt_it5629HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion716SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4670SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.51
X-RAY DIFFRACTIONt_other_torsion16.82
LS refinement shellResolution: 1.941→1.96 Å
RfactorNum. reflection% reflection
Rfree0.2829 63 -
Rwork0.2414 --
obs--93.87 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.82070.83160.36181.0956-0.32320.4239-0.02580.0254-0.00210.0254-0.0060.0112-0.00210.01120.0318-0.0335-0.0054-0.00950.00280.0301-0.045438.668410.37344.6183
20.730.24950.00651.012-0.48471.1878-0.0320.0724-0.1170.07240.00180.0996-0.1170.09960.03020.01640.0105-0.003-0.01110.0045-0.065443.65849.274816.6507
30.5732-0.0928-0.12881.3815-0.45070.8412-0.16270.10520.0120.10520.00830.05550.0120.05550.1545-0.07010.00270.0586-0.0110.04380.022916.085748.777347.1359
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ C|* }C183 - 399
2X-RAY DIFFRACTION1{ C|* }C801
3X-RAY DIFFRACTION2{ F|* }F180 - 399
4X-RAY DIFFRACTION2{ F|* }F801
5X-RAY DIFFRACTION3{ G|* }G181 - 399
6X-RAY DIFFRACTION3{ G|* }G801

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