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

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Basic information

Entry
Database: PDB / ID: 7qty
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
1-(furan-2-ylmethyl)-3-(2-methylphenyl)thiourea / FLAVIN-ADENINE DINUCLEOTIDE / Na(+)-translocating NADH-quinone reductase subunit F
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 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)33,2044
Polymers32,0941
Non-polymers1,1103
Water5,603311
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-7 kcal/mol
Surface area13380 Å2
Unit cell
Length a, b, c (Å)98.545, 98.545, 89.595
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw

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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: fragment residues 129-407
Source method: isolated from a genetically manipulated source
Details: N-terminal residues Gly and Pro originate from expression tag
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-F0R / 1-(furan-2-ylmethyl)-3-(2-methylphenyl)thiourea


Mass: 246.328 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H14N2OS
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 3.39 Å3/Da / Density % sol: 63.7 %
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: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.69→49.27 Å / Num. obs: 50089 / % possible obs: 100 % / Redundancy: 20 % / Biso Wilson estimate: 30.03 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1 / Rrim(I) all: 0.102 / Χ2: 0.841 / Net I/σ(I): 21.71
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.69-1.8201.82.4384620.8012.182100
1.8-1.926.9421.2824.5760830.9261.307100
1.9-225.1810.7727.3949460.9720.788100
2-326.5790.19121.53211130.9980.195100
3-427.2060.06454.8552540.9980.065100
4-624.2410.04962.5127770.9990.05100
6-1026.0990.04165.4496310.042100
10-49.2721.8930.03364.3429810.03399

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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: pdbid 4UAJ

4uaj


Resolution: 1.69→49.27 Å / SU ML: 0.2457 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.6926
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1997 2501 4.99 %
Rwork0.1749 47584 -
obs0.1761 50085 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.4 Å2
Refinement stepCycle: LAST / Resolution: 1.69→49.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2252 0 74 311 2637
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00672427
X-RAY DIFFRACTIONf_angle_d0.89873309
X-RAY DIFFRACTIONf_chiral_restr0.0618333
X-RAY DIFFRACTIONf_plane_restr0.0093429
X-RAY DIFFRACTIONf_dihedral_angle_d12.8102331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.720.411330.38932529X-RAY DIFFRACTION97.26
1.72-1.750.35461370.30752607X-RAY DIFFRACTION100
1.75-1.790.27131370.26622605X-RAY DIFFRACTION100
1.79-1.830.26041370.22582614X-RAY DIFFRACTION100
1.83-1.880.21221370.19482598X-RAY DIFFRACTION100
1.88-1.930.21511380.18232627X-RAY DIFFRACTION99.96
1.93-1.990.2241370.18382618X-RAY DIFFRACTION99.96
1.99-2.050.21731380.19462610X-RAY DIFFRACTION100
2.05-2.130.24421360.21022611X-RAY DIFFRACTION100
2.13-2.210.19451390.16132627X-RAY DIFFRACTION100
2.21-2.310.19541380.1752633X-RAY DIFFRACTION100
2.31-2.430.21751400.1812647X-RAY DIFFRACTION100
2.43-2.590.2461390.18392651X-RAY DIFFRACTION100
2.59-2.790.23681400.1932642X-RAY DIFFRACTION100
2.79-3.070.21541400.17982674X-RAY DIFFRACTION100
3.07-3.510.18841430.16512697X-RAY DIFFRACTION100
3.51-4.420.15271430.13672720X-RAY DIFFRACTION100
4.42-49.270.17341490.16562874X-RAY DIFFRACTION99.93
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)
12.232128979850.71794217295-0.3267308080782.143180741670.1331207370182.37731470962-0.1039483895190.0284128061102-0.1324846119610.02505657531150.02765224263380.292296327945-0.0216104871889-0.5958342458180.06007608420830.214753908598-0.03019606626290.006151502964980.3329153126270.01976292233570.244367905956-19.903769429528.075593593313.973336416
20.758162050806-0.199927141292-0.3550444283750.603110468245-0.1183455628672.139794185010.0939031163805-0.0626337365453-0.3169668032740.09256836025430.02904714808920.006572404764140.287168810965-0.309647523931-0.1425953723470.235942745952-0.0447196609024-0.005520308210720.2367851389350.03383952408010.249118544935-14.13865665424.073767051612.7871929586
31.471732667940.364597911965-0.1534561240381.418160002231.218411803931.682621663490.0376760774828-0.2106681820940.103598945008-0.0684951101642-0.09845666855150.157072893346-0.18191937207-0.3820194613730.06381497237990.2132362295520.0182269375722-0.008210684864570.2103972501020.01401919140.198542597393-13.181038376438.690729941116.0751023879
43.487837625911.111201740870.4810443296143.039569660951.478075893463.01471157068-0.08757756582550.04099494024290.342200966131-0.06417605761770.0217958452265-0.235080303004-0.2344783946560.1953027657980.01926266567780.264192078876-0.007454597039660.02383764806510.2264955867680.0320531171810.193492204642-2.5689847077342.968694025618.9899403293
52.034504839610.3425552628710.01799508146932.61953792831-0.2693503138032.99693256893-0.06888520188550.068547934371-0.301666789162-0.210637001530.02533024815530.04527881211070.198151126213-0.211564399014-0.007567495006530.240685456115-0.0248675594412-0.01728650947630.2507552397310.002572492287270.263554572197-14.167554802824.22474658568.20197703144
62.912735558390.5609409238070.7658991920556.00023729194-1.216259904892.449462581570.03195383438170.07458025552090.1761737212870.497677647116-0.25016368672-0.663663355221-0.37882665680.2214939367830.2113788047030.238947074718-0.0162844009914-0.005244921647360.2475185779420.004861484246820.217489944739-5.2932440500340.155869623510.3942494268
72.259204677010.03169711052770.2354212469491.067746601870.6003285519680.9240617317860.03544865136190.233500831743-0.147602431976-0.146622647289-0.0002540457327940.0250243336750.107311866501-0.197404967218-0.008977940392580.223926035582-0.0347172756069-0.01185396674350.2085427634130.03212212971520.170214585358-13.09354660627.97138325777.22628109835
82.54238310855-0.00591213913165-0.7277081727310.8254838120550.4519306658530.882338055912-0.01313343514930.179879201301-0.655757151149-0.1299969341320.0369160183038-0.07587523075430.225360815933-0.0208009713807-0.01444937560960.2878541197720.00354842527853-0.01496273107820.256418576709-0.05836316979030.363090880419-2.2425106220516.61689154842.63689874027
92.050155097780.6641837934550.03970118270351.598288210161.092246341531.660680960550.0264456288479-0.0493253051494-0.3920042869960.2078818490190.12714593427-0.05827993435420.3265717459360.147857319403-0.1772830882440.2704160247250.0420283303481-0.01917492842450.227205714325-0.02302136766580.3236614579034.6139865615117.933625464910.4446235602
101.547999019560.9462994424281.036357742360.9593581585560.9074738868714.45410287078-0.0009694531939240.256166802959-0.04626942451870.04989695188650.126803657762-0.2608923039530.4271772617240.764532448469-0.1993824260690.2424990337610.06621641905410.007053048102490.333545767655-0.07069271159570.28411232277514.886817651525.85687378486.3116622556
112.19422733738-0.582424560592-0.5116147648371.035220476160.1343436554781.149205019660.241227198110.622626525952-0.342246136792-0.303888304311-0.208441887305-0.1763426319520.2138153401020.0894261126706-0.06558506958690.3656458577770.04536097088530.01693675467890.423530551719-0.1389997354690.3349512436776.0461053683218.7463417555-7.68802200815
123.14540132487-0.722706623124-0.4264727898043.124492636650.3545163982893.59374641790.1484869618020.7952303917160.0432901662103-0.45663043612-0.156472742850.0366662430160.0437628508161-0.1642475728020.03525864902160.3029102486690.05935439496570.01378485958220.3887434051360.0009723240871170.2393336332192.0007745224327.6622978141-8.54719487516
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 127 through 141 )127 - 1411 - 15
22chain 'A' and (resid 142 through 165 )142 - 16516 - 39
33chain 'A' and (resid 166 through 184 )166 - 18440 - 58
44chain 'A' and (resid 185 through 206 )185 - 20659 - 80
55chain 'A' and (resid 207 through 221 )207 - 22181 - 95
66chain 'A' and (resid 222 through 242 )222 - 24296 - 116
77chain 'A' and (resid 243 through 274 )243 - 274117 - 148
88chain 'A' and (resid 275 through 310 )275 - 310149 - 184
99chain 'A' and (resid 311 through 338 )311 - 338185 - 212
1010chain 'A' and (resid 339 through 361 )339 - 361213 - 235
1111chain 'A' and (resid 362 through 379 )362 - 379236 - 253
1212chain 'A' and (resid 380 through 405 )380 - 405254 - 279

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