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- PDB-6hl4: wild-type NuoEF from Aquifex aeolicus - reduced form -

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Basic information

Entry
Database: PDB / ID: 6hl4
Titlewild-type NuoEF from Aquifex aeolicus - reduced form
Components(NADH-quinone oxidoreductase subunit ...) x 2
KeywordsELECTRON TRANSPORT / Complex I / NuoEF / electron transfer / Aquifex aeolicus
Function / homology
Function and homology information


Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH dehydrogenase (ubiquinone) activity / quinone binding / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / FMN binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / metal ion binding
Similarity search - Function
Soluble ligand binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit / Ubiquitin-like (UB roll) - #600 / SLBB domain / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NuoE domain / NADH-quinone oxidoreductase subunit E-like / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. ...Soluble ligand binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit / Ubiquitin-like (UB roll) - #600 / SLBB domain / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NuoE domain / NADH-quinone oxidoreductase subunit E-like / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-quinone oxidoreductase subunit E, N-terminal / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / Thioredoxin-like [2Fe-2S] ferredoxin / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Nuo51 FMN-binding domain / Ubiquitin-like (UB roll) / Thioredoxin-like superfamily / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / IRON/SULFUR CLUSTER / NADH-quinone oxidoreductase subunit F / NADH-quinone oxidoreductase subunit E
Similarity search - Component
Biological speciesAquifex aeolicus VF5 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsGerhardt, S. / Friedrich, T. / Einsle, O. / Gnandt, E. / Schulte, M. / Fiegen, D.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationRTG 2202 Germany
CitationJournal: Nat Commun / Year: 2019
Title: A mechanism to prevent production of reactive oxygen species by Escherichia coli respiratory complex I.
Authors: Schulte, M. / Frick, K. / Gnandt, E. / Jurkovic, S. / Burschel, S. / Labatzke, R. / Aierstock, K. / Fiegen, D. / Wohlwend, D. / Gerhardt, S. / Einsle, O. / Friedrich, T.
History
DepositionSep 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADH-quinone oxidoreductase subunit E
B: NADH-quinone oxidoreductase subunit F
C: NADH-quinone oxidoreductase subunit E
D: NADH-quinone oxidoreductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,19711
Polymers134,1944
Non-polymers2,0037
Water2,288127
1
A: NADH-quinone oxidoreductase subunit E
B: NADH-quinone oxidoreductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1166
Polymers67,0972
Non-polymers1,0194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint-82 kcal/mol
Surface area21570 Å2
MethodPISA
2
C: NADH-quinone oxidoreductase subunit E
D: NADH-quinone oxidoreductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0815
Polymers67,0972
Non-polymers9843
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint-72 kcal/mol
Surface area21300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.741, 108.117, 188.181
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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NADH-quinone oxidoreductase subunit ... , 2 types, 4 molecules ACBD

#1: Protein NADH-quinone oxidoreductase subunit E / NADH dehydrogenase I subunit E / NDH-1 subunit E


Mass: 18573.619 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Gene: nuoE, aq_574 / Production host: Escherichia coli (E. coli) / References: UniProt: O66842, NADH dehydrogenase (quinone)
#2: Protein NADH-quinone oxidoreductase subunit F / NADH dehydrogenase I subunit F / NDH-1 subunit F


Mass: 48523.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: sequence contains C-terminal 6xHis-Expressiontag / Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Gene: nuoF, aq_573 / Production host: Escherichia coli (E. coli) / References: UniProt: O66841, NADH dehydrogenase (quinone)

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Non-polymers , 5 types, 134 molecules

#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O

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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: 45.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.9 / Details: 0.1M Tris/HCl 0.1M Sodium citrate / PH range: 6.9 - 7.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54179 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.06→188.18 Å / Num. obs: 65727 / % possible obs: 86.7 % / Redundancy: 4.9 % / Biso Wilson estimate: 24.22 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.06 / Rrim(I) all: 0.135 / Net I/σ(I): 9.3
Reflection shellResolution: 2.06→2.18 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 7715 / CC1/2: 0.795 / Rpim(I) all: 0.242 / Rrim(I) all: 0.42 / % possible all: 71.1

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
autoPROCdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IN-HOUSE

Resolution: 2.06→36.96 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.9 / SU R Cruickshank DPI: 0.251 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.243 / SU Rfree Blow DPI: 0.187 / SU Rfree Cruickshank DPI: 0.192
RfactorNum. reflection% reflectionSelection details
Rfree0.237 3277 4.99 %RANDOM
Rwork0.205 ---
obs0.207 65618 86.7 %-
Displacement parametersBiso mean: 33.08 Å2
Baniso -1Baniso -2Baniso -3
1-1.4146 Å20 Å20 Å2
2---5.6665 Å20 Å2
3---4.2519 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: 1 / Resolution: 2.06→36.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9053 0 87 127 9267
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0089371HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9812704HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3234SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1610HARMONIC5
X-RAY DIFFRACTIONt_it9371HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.59
X-RAY DIFFRACTIONt_other_torsion20
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1181SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11364SEMIHARMONIC4
LS refinement shellResolution: 2.06→2.09 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2269 -5.41 %
Rwork0.2209 1242 -
all0.2212 1313 -
obs--46.5 %
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)
10.63260.23350.4610-0.0012.3373-0.0301-0.23370.4715-0.0254-0.00290.0566-0.53080.01310.0331-0.01110.0258-0.0256-0.0714-0.0751-0.0606-6.946910.9784-10.5622
21.5866-0.15970.53230.1379-0.10621.24110.0928-0.117-0.12290.0022-0.00140.10780.07130.1319-0.0914-0.05880.0072-0.0496-0.0288-0.016-0.1059-7.1908-12.2853-16.3992
33.3805-0.46550.15751.17650.08211.0585-0.01930.3169-0.3249-0.0206-0.00110.07510.27620.04860.02040.0048-0.0208-0.0035-0.1102-0.0085-0.104522.6711-11.5367-59.1934
41.19560.0226-0.19210.3778-0.03871.23720.04540.02340.1621-0.02110.0112-0.0089-0.0250.0488-0.0566-0.0599-0.003-0.0119-0.06440.0317-0.079622.396511.5473-52.5491
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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