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- PDB-7qu0: X-ray structure of FAD domain of NqrF of Klebsiella pneumoniae -

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Basic information

Entry
Database: PDB / ID: 7qu0
TitleX-ray structure of FAD domain of NqrF of Klebsiella pneumoniae
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 / Flavoprotein pyridine nucleotide cytochrome reductase / Oxidoreductase FAD/NAD(P)-binding ...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 / Flavoprotein pyridine nucleotide cytochrome reductase / 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
~{N}-[2,6-bis(fluoranyl)phenyl]ethanamide / FLAVIN-ADENINE DINUCLEOTIDE / Na(+)-translocating NADH-quinone reductase subunit F
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 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)33,2075
Polymers32,0941
Non-polymers1,1134
Water4,252236
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-7 kcal/mol
Surface area13620 Å2
Unit cell
Length a, b, c (Å)98.840, 98.840, 88.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-818-

HOH

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Components

#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: 32094.436 Da / Num. of mol.: 1 / Fragment: FAD binding domain / Mutation: residues 129-407
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.) Klebsiella pneumoniae (bacteria) / Strain: ATCC 700721 / MGH 78578 / Gene: nqrF, KPN78578_02360, KPN_00244 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A6T526, NADH:ubiquinone reductase (Na+-transporting)
#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-F2L / ~{N}-[2,6-bis(fluoranyl)phenyl]ethanamide


Mass: 171.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H7F2NO
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O
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: 3.38 Å3/Da / Density % sol: 63.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7 / Details: 1.75 M tri-ammonium citrat, 0.1 M LiSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.62→43.18 Å / Num. obs: 55906 / % possible obs: 99.3 % / Redundancy: 26.43 % / Biso Wilson estimate: 22.83 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.121 / Rrim(I) all: 0.123 / Χ2: 0.796 / Net I/σ(I): 22.28
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
1.62-1.826.41.8482.0438594815017146190.7351.88597.3
1.8-1.927.5840.9334.29167575607560750.9230.951100
1.9-227.0870.5846.85132806490449030.9680.595100
2-326.4060.18220.2855597221055210550.9980.186100
3-425.4510.0565.951332625236523610.051100
4-625.5310.03294.94705692765276410.032100
6-1026.3860.0395.782538396296210.031100
10-43.1820.8120.024100.42597330028710.02495.7

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Processing

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

4uaj


Resolution: 1.62→43.18 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.193 2794 5 %
Rwork0.1675 53108 -
obs0.1687 55902 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.21 Å2 / Biso mean: 29.2747 Å2 / Biso min: 14.82 Å2
Refinement stepCycle: final / Resolution: 1.62→43.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2252 0 85 236 2573
Biso mean--28.14 39.39 -
Num. residues----279
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.62-1.650.31811330.282522265597
1.65-1.680.25571380.253526182756100
1.68-1.710.27711370.235126062743100
1.71-1.750.24581390.216426482787100
1.75-1.790.24491370.211625942731100
1.79-1.830.25131370.208526352772100
1.83-1.870.22071380.185326282766100
1.87-1.920.18341390.167426332772100
1.92-1.980.16741390.15226382777100
1.98-2.040.18411370.150826322769100
2.05-2.120.16691380.150326472785100
2.12-2.20.18171390.146226322771100
2.2-2.30.19131410.154826722813100
2.3-2.420.18381390.155126432782100
2.42-2.580.17111400.159526632803100
2.58-2.780.1781410.164126792820100
2.78-3.050.17721420.160926862828100
3.05-3.50.18441430.157327182861100
3.5-4.40.17151430.14727302873100
4.4-43.180.21791540.186328843038100
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)
12.07160.9104-0.1191.79990.15662.4023-0.03040.02160.0657-0.0550.00690.10730.0789-0.44630.01950.1898-0.01010.01640.23260.02230.1874-19.73427.940713.93
21.5220.23760.23340.87440.09781.49520.0844-0.0929-0.29140.05180.0099-0.07030.1991-0.1838-0.0910.1774-0.01510.01330.17240.01840.19-13.64124.274212.3352
30.81290.3628-0.09111.05830.78011.02370.0011-0.07640.1385-0.0406-0.08940.1403-0.1044-0.18510.07240.19420.0161-0.00690.19570.00960.2088-13.890438.307115.413
43.63231.14731.11992.15390.68182.2786-0.1055-0.04890.2419-0.09380.0589-0.1712-0.25880.15990.02950.2279-0.01410.01280.20130.01560.1606-3.063243.475818.9586
51.7205-0.32920.0352.19560.07471.9857-0.05570.0736-0.2372-0.0532-0.02520.07340.0694-0.11510.06740.1721-0.00520.00510.2074-0.00720.212-14.041324.22788.1228
60.87090.20860.3611.9506-0.68941.8345-0.04240.02040.07460.0184-0.0451-0.1239-0.1930.1250.08130.1773-0.0107-0.00240.18650.00860.1953-7.256539.781611.6515
71.3305-0.12180.59380.5024-0.20610.4790.14880.2828-0.1938-0.1944-0.04340.0348-0.0764-0.197-0.09640.2209-0.0384-0.01080.2254-0.01480.2249-13.571423.96254.182
81.5843-0.002-0.21651.02480.4590.7828-0.06410.0938-0.3704-0.130.07690.03490.06840.0197-0.00760.21450.00940.02030.2199-0.04820.283-2.109916.76762.3879
91.61680.07050.04892.10041.06531.4986-0.0598-0.1391-0.14590.25590.1151-0.07910.19290.1796-0.04050.19910.03220.00660.2126-0.01150.20934.873518.083310.3071
101.13160.60180.65990.83050.78733.6608-0.02590.07730.09440.06150.1332-0.23530.2450.6063-0.15920.21230.03980.00180.2836-0.04460.253515.005126.40326.2376
112.031-0.44210.06982.8163-0.07461.92060.21120.67930.0187-0.4299-0.32180.0116-0.0129-0.13270.10610.29410.04650.01830.3937-0.02380.23753.942423.8634-8.5756
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 127 through 141 )A127 - 141
2X-RAY DIFFRACTION2chain 'A' and (resid 142 through 165 )A142 - 165
3X-RAY DIFFRACTION3chain 'A' and (resid 166 through 184 )A166 - 184
4X-RAY DIFFRACTION4chain 'A' and (resid 185 through 206 )A185 - 206
5X-RAY DIFFRACTION5chain 'A' and (resid 207 through 221 )A207 - 221
6X-RAY DIFFRACTION6chain 'A' and (resid 222 through 250 )A222 - 250
7X-RAY DIFFRACTION7chain 'A' and (resid 251 through 274 )A251 - 274
8X-RAY DIFFRACTION8chain 'A' and (resid 275 through 310 )A275 - 310
9X-RAY DIFFRACTION9chain 'A' and (resid 311 through 338 )A311 - 338
10X-RAY DIFFRACTION10chain 'A' and (resid 339 through 361 )A339 - 361
11X-RAY DIFFRACTION11chain 'A' and (resid 362 through 405 )A362 - 405

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