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- PDB-7qu3: X-ray structure of FAD domain of NqrF of Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 7qu3
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 / 4-(benzimidazol-1-ylmethyl)benzenecarbonitrile / Na(+)-translocating NADH-quinone reductase subunit F
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
Model detailsin complex with 3-[(furan-2-yl)methyl]-1-(2-methylphenyl)thiourea
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)33,4098
Polymers32,0531
Non-polymers1,3567
Water4,161231
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-6 kcal/mol
Surface area12860 Å2
Unit cell
Length a, b, c (Å)49.543, 57.669, 101.440
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: N-terminal residues Gly and Pro originate from N-terminal purification tag (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, 238 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-RYM / 4-(benzimidazol-1-ylmethyl)benzenecarbonitrile


Mass: 233.268 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H11N3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.26 Å3/Da / Density % sol: 45.59 %
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 EIGER X 16M / Detector: PIXEL / Date: Apr 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→44.52 Å / Num. obs: 38938 / % possible obs: 99.2 % / Redundancy: 13.147 % / Biso Wilson estimate: 24.84 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.069 / Χ2: 0.883 / Net I/σ(I): 20.13 / Num. measured all: 511924 / Scaling rejects: 17
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
1.6-1.812.4381.0232.5814077811586113180.861.06797.7
1.8-1.913.3620.4266.354411407740720.9680.44399.9
1.9-214.1660.26310.5646664329432940.9860.273100
2-313.6590.09824.0819211214081140650.9990.10299.9
3-412.1890.0452.2942539351034900.9990.04299.4
4-613.5370.03264.83251121855185510.033100
6-1012.7220.03163.33824464864810.032100
10-44.5210.5310.02960.720641981960.9990.03199

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
PHENIX1.20_4459refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UAJ

4uaj


Resolution: 1.6→44.52 Å / SU ML: 0.2206 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.6713
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1962 1947 5 %
Rwork0.1711 36989 -
obs0.1724 38936 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.81 Å2
Refinement stepCycle: LAST / Resolution: 1.6→44.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2254 0 88 231 2573
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01492458
X-RAY DIFFRACTIONf_angle_d1.31063352
X-RAY DIFFRACTIONf_chiral_restr0.0867330
X-RAY DIFFRACTIONf_plane_restr0.0118436
X-RAY DIFFRACTIONf_dihedral_angle_d11.8881336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.36921260.32522404X-RAY DIFFRACTION92.54
1.64-1.680.31111380.29362616X-RAY DIFFRACTION99.42
1.68-1.730.29151380.2352616X-RAY DIFFRACTION99.53
1.73-1.790.2551370.1982598X-RAY DIFFRACTION99.27
1.79-1.850.19861380.1842630X-RAY DIFFRACTION99.57
1.85-1.930.21881380.18152624X-RAY DIFFRACTION100
1.93-2.010.21581400.18372651X-RAY DIFFRACTION100
2.01-2.120.19161390.16082644X-RAY DIFFRACTION100
2.12-2.250.21391400.1622657X-RAY DIFFRACTION100
2.25-2.430.21911380.1722640X-RAY DIFFRACTION100
2.43-2.670.24211410.18662670X-RAY DIFFRACTION100
2.67-3.060.18891420.17922684X-RAY DIFFRACTION99.33
3.06-3.850.18741410.15632704X-RAY DIFFRACTION99.44
3.85-44.520.15281510.14992851X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / 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)
10.18848033029-0.247993316997-0.2659875337230.8813176316850.0115500881591.050344771470.06891802630290.001082486194930.318306174317-0.08913512238710.0912084649207-0.0504795416293-0.2289696700780.02070128767070.00019044940190.202200093724-0.01907833949170.02688601702570.216905899907-0.01635641548080.24553272030816.3505718208-5.89945844281-13.3144395468
20.9132876977810.27183733693-0.04438372206630.2001131618820.3969472379431.246804034470.0842556985972-0.08485669288270.1720874927890.005543752448910.0426418802756-0.0279430525036-0.2147295206830.193227793020.0001182921611280.182558945192-0.01793201997060.02107928602590.2016563700370.009255165460990.23082444915718.1709345671-9.34433540423-11.1211665925
30.8294725292620.285565704909-0.8200908236490.582681571344-0.03023188480750.919821572968-0.0549357309839-0.048725414776-0.2323700186230.07176343358750.02745427395220.09917534119660.0991789988548-0.1504188539696.88221818646E-50.19837748644-0.0189354244057-0.007832686414170.237760769135-0.01983803587050.2245300521916.10247408417-18.7422748322-4.67397842301
40.1727435823830.072541662761-0.0916335691540.3993146307110.2005933681340.666722336676-0.104085983803-0.04096486754540.1230522804490.3555133416820.0463957109708-0.0498697678884-0.6933044768610.367162215331-0.003666143536050.341525846323-0.0460524088567-0.01871005641140.197643655365-0.002297066495470.2751974348218.8648901954-6.63825997828-20.6774454386
50.1792969260310.02591352822020.04636255876050.3190798695720.5459518885280.9218022205160.09335561412770.0582577269919-0.09475576978930.0312249424677-0.02836241275780.2876092830330.0719403448220.120550362755-0.0002579504252760.169683306463-0.00526779194081-0.004417234583720.1913232575890.01125889658180.25695814900311.3045477644-19.3885172599-11.3937479589
60.6583810290190.5130591892410.2551987206340.4904075549140.6065333810691.35860102804-0.09755664799560.1041178771910.0963159530328-0.1876377980980.0808027492565-0.0110347609437-0.2817025942090.140437715819-0.0001645675611210.250042689202-0.004802123484180.0104300809450.1809232767220.01759685885720.21232994893614.1190508316-9.08647954474-26.3899091423
71.173615504141.018734440180.7921212186541.193403055010.3336279095860.970943596580.0952521150401-0.2062504498260.04433439580650.138433458513-0.3075002640470.230098126381-0.435136463778-0.424563572365-0.2764903906750.3163983372420.149976915084-0.01437650359690.2323066398120.0006944109688050.2155747598550.713483099151-5.87419013323-25.4075609095
80.821055346798-0.148502186780.5503986816010.7657070979430.2803074914620.545337449607-0.1879279311530.187986133597-0.0938248002966-0.1469914069730.01453908481470.271632241132-0.0899210582521-0.501164172143-0.01501059062580.2863016259140.0352178076989-0.023729999740.2670752267270.01116757578920.269803304619-4.99966535661-12.7818827873-28.9085050025
91.114885041750.185774504398-0.6412380228740.9008091769340.01156784067881.32257205839-0.07249185448370.243948318755-0.430666414094-0.188460325237-0.0030766613756-0.1666625366040.3638181921210.173855964862-1.9085689261E-50.349544202070.02058547971470.02513338873570.238586207415-0.04667992025920.2625830572747.92936364799-21.6138159012-37.2029716059
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 128 through 153 )128 - 1531 - 26
22chain 'A' and (resid 154 through 185 )154 - 18527 - 58
33chain 'A' and (resid 186 through 207 )186 - 20759 - 80
44chain 'A' and (resid 208 through 222 )208 - 22281 - 95
55chain 'A' and (resid 223 through 242 )223 - 24296 - 115
66chain 'A' and (resid 243 through 310 )243 - 310116 - 183
77chain 'A' and (resid 311 through 328 )311 - 328184 - 201
88chain 'A' and (resid 329 through 353 )329 - 353202 - 226
99chain 'A' and (resid 354 through 406 )354 - 406227 - 279

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