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- PDB-7qu5: X-ray structure of FAD domain of NqrF of Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 7qu5
TitleX-ray structure of FAD domain of NqrF of Pseudomonas aeruginosa
ComponentsNa(+)-translocating NADH-quinone reductase subunit F
KeywordsFLAVOPROTEIN / NADH oxidizing
Function / homology
Function and homology information


NADH:ubiquinone reductase (Na+-transporting) / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / sodium ion transport / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / membrane => GO:0016020 / electron transfer activity / metal ion binding / plasma membrane
Similarity search - Function
Na(+)-translocating NADH-quinone reductase subunit F / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain ...Na(+)-translocating NADH-quinone reductase subunit F / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 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 / gamma-Valerolactone / Na(+)-translocating NADH-quinone reductase subunit F
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
Model detailsin complex with 5-methyloxolan-2-one
AuthorsStegmann, D. / Steuber, J. / Fritz, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Fast fragment- and compound-screening pipeline at the Swiss Light Source.
Authors: Kaminski, J.W. / Vera, L. / Stegmann, D.P. / Vering, J. / Eris, D. / Smith, K.M.L. / Huang, C.Y. / Meier, N. / Steuber, J. / Wang, M. / Fritz, G. / Wojdyla, J.A. / Sharpe, M.E.
History
DepositionJan 17, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Na(+)-translocating NADH-quinone reductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2988
Polymers32,0531
Non-polymers1,2447
Water6,341352
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-9 kcal/mol
Surface area12950 Å2
Unit cell
Length a, b, c (Å)49.358, 59.908, 102.390
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Na(+)-translocating NADH-quinone reductase subunit F / Na(+)-NQR subunit F / Na(+)-translocating NQR subunit F / NQR complex subunit F / NQR-1 subunit F


Mass: 32053.072 Da / Num. of mol.: 1 / Fragment: FAD binding domain / Mutation: residues 130-407
Source method: isolated from a genetically manipulated source
Details: The N-terminal residues Gly and Pro are residual from the N-terminal His-tag after Prescission protease cleavage
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: UCBPP-PA14 / Gene: nqrF, PA14_25350 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q02PF8, NADH:ubiquinone reductase (Na+-transporting)

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Non-polymers , 5 types, 359 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-YVR / gamma-Valerolactone


Mass: 100.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H8O2
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.36 Å3/Da / Density % sol: 47.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6 / Details: 0.1M MES, PEG 4000, 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→38.92 Å / Num. obs: 84539 / % possible obs: 99.5 % / Redundancy: 11.92 % / Biso Wilson estimate: 15.66 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.068 / Χ2: 0.852 / Net I/σ(I): 20.47
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.25-1.811.3720.5035.1262985555789553870.970.52799.3
1.8-1.913.4750.13321.6657486426642660.9970.138100
1.9-213.1530.09529.1745088342834280.9980.099100
2-313.0570.04949.0319202314707147070.9990.051100
3-412.320.02778.08450053653365310.029100
4-612.4750.02386.29242011941194010.02499.9
6-1012.8890.02387.83862366966910.024100
10-38.9210.0150.02379.7320232042020.9990.02499

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Processing

Software
NameVersionClassification
PHENIX1.2refinement
PHENIX1.2refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UAJ

4uaj


Resolution: 1.25→38.92 Å / SU ML: 0.1689 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.7636
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1741 4225 5 %
Rwork0.1436 80282 -
obs0.1452 84507 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.72 Å2
Refinement stepCycle: LAST / Resolution: 1.25→38.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2259 0 80 352 2691
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01052500
X-RAY DIFFRACTIONf_angle_d1.08153412
X-RAY DIFFRACTIONf_chiral_restr0.0958337
X-RAY DIFFRACTIONf_plane_restr0.0096449
X-RAY DIFFRACTIONf_dihedral_angle_d12.8851342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.260.40211270.41552409X-RAY DIFFRACTION91.45
1.26-1.280.41541320.37882515X-RAY DIFFRACTION94.74
1.28-1.290.3281370.34652597X-RAY DIFFRACTION97.54
1.29-1.310.35891390.29822663X-RAY DIFFRACTION99.64
1.31-1.330.31311390.27082623X-RAY DIFFRACTION99.78
1.33-1.340.27121400.24542659X-RAY DIFFRACTION99.89
1.34-1.360.25621410.21812693X-RAY DIFFRACTION99.93
1.36-1.380.24581380.19662628X-RAY DIFFRACTION99.93
1.38-1.410.22361410.18582675X-RAY DIFFRACTION100
1.41-1.430.24631400.18862667X-RAY DIFFRACTION99.96
1.43-1.450.22891410.17612670X-RAY DIFFRACTION100
1.45-1.480.21361390.1742652X-RAY DIFFRACTION99.96
1.48-1.510.21551400.16472655X-RAY DIFFRACTION100
1.51-1.540.161430.14072711X-RAY DIFFRACTION100
1.54-1.570.1971390.13332643X-RAY DIFFRACTION99.96
1.57-1.610.16961420.11892692X-RAY DIFFRACTION100
1.61-1.650.16141420.10522711X-RAY DIFFRACTION100
1.65-1.690.15851400.10172662X-RAY DIFFRACTION100
1.69-1.740.15271400.10012656X-RAY DIFFRACTION100
1.74-1.80.16271420.1062695X-RAY DIFFRACTION100
1.8-1.860.16321420.1162696X-RAY DIFFRACTION100
1.86-1.940.16581420.11562690X-RAY DIFFRACTION100
1.94-2.030.15691420.1092698X-RAY DIFFRACTION100
2.03-2.130.14181420.10782706X-RAY DIFFRACTION100
2.13-2.270.13941430.11672723X-RAY DIFFRACTION100
2.27-2.440.15771420.12732702X-RAY DIFFRACTION100
2.44-2.690.17611450.14242739X-RAY DIFFRACTION100
2.69-3.080.17151440.14462751X-RAY DIFFRACTION100
3.08-3.880.17281470.13862781X-RAY DIFFRACTION100
3.88-38.920.14531540.15222920X-RAY DIFFRACTION99.93

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