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- PDB-6q9k: Crystal structure of reduced Aquifex aeolicus NADH-quinone oxidor... -

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Basic information

Entry
Database: PDB / ID: 6q9k
TitleCrystal structure of reduced Aquifex aeolicus NADH-quinone oxidoreductase subunits NuoE and NuoF S96M bound to NADH
Components(NADH-quinone oxidoreductase subunit ...) x 2
KeywordsOXIDOREDUCTASE / respiratory chain / complex I / NADH ubiquinone oxidoreductase / Fe-S clusters
Function / homology
Function and homology information


Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / quinone binding / 2 iron, 2 sulfur cluster binding / FMN binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / metal ion binding
Similarity search - Function
Ubiquitin-like (UB roll) - #600 / NADH-ubiquinone oxidoreductase 51kDa subunit / Soluble ligand binding domain / SLBB domain / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / 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 ...Ubiquitin-like (UB roll) - #600 / NADH-ubiquinone oxidoreductase 51kDa subunit / Soluble ligand binding domain / SLBB domain / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / 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 / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Respiratory-chain NADH dehydrogenase 51 Kd subunit / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NuoE domain / NADH-quinone oxidoreductase subunit E-like / NADH-quinone oxidoreductase subunit E, N-terminal / Thioredoxin-like [2Fe-2S] ferredoxin / 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 / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / IRON/SULFUR CLUSTER / NADH-quinone oxidoreductase subunit F / NADH-quinone oxidoreductase subunit E
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.99 Å
AuthorsWohlwend, D. / Gerhardt, S. / Gnandt, E. / Friedrich, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationRTG 1976 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
DepositionDec 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)133,69726
Polymers129,4344
Non-polymers4,26222
Water17,276959
1
A: NADH-quinone oxidoreductase subunit E
B: NADH-quinone oxidoreductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,88113
Polymers64,7172
Non-polymers2,16411
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7880 Å2
ΔGint-124 kcal/mol
Surface area21370 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17270 Å2
ΔGint-265 kcal/mol
Surface area41110 Å2
MethodPISA
3
C: NADH-quinone oxidoreductase subunit E
D: NADH-quinone oxidoreductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,81613
Polymers64,7172
Non-polymers2,09811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7970 Å2
ΔGint-146 kcal/mol
Surface area21160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.380, 115.940, 189.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 17935.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Strain: VF5 / Gene: nuoE, aq_574 / Plasmid: pETBlue-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: O66842, NADH dehydrogenase (quinone)
#2: Protein NADH-quinone oxidoreductase subunit F / NADH dehydrogenase I subunit F / NDH-1 subunit F


Mass: 46781.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Strain: VF5 / Gene: nuoF, aq_573 / Plasmid: pETBlue-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: O66841, NADH dehydrogenase (quinone)

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Non-polymers , 8 types, 981 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


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


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#7: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 959 / 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: 2.7 Å3/Da / Density % sol: 54.41 % / Mosaicity: 0.68 °
Crystal growTemperature: 281 K / Method: evaporation / pH: 6.25
Details: (NH4)2SO4, BisTris, NaCl, cryo-protection with glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.99→21.26 Å / Num. obs: 96646 / % possible obs: 99.8 % / Redundancy: 5.8 % / CC1/2: 0.992 / Rmerge(I) obs: 0.182 / Rpim(I) all: 0.081 / Rrim(I) all: 0.2 / Net I/σ(I): 6.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.99-2.0250.86746990.6990.4030.96199.3
10.9-21.255.70.0655840.9970.0280.07186.7

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Processing

Software
NameVersionClassification
REFMACrefinement
Aimless0.7.3data scaling
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.99→21.26 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 7.997 / SU ML: 0.123 / SU R Cruickshank DPI: 0.1728 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.149
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2186 4988 5.2 %RANDOM
Rwork0.1879 ---
obs0.1895 91590 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 74.9 Å2 / Biso mean: 21.726 Å2 / Biso min: 8.42 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20 Å20 Å2
2--0.29 Å2-0 Å2
3----0.98 Å2
Refinement stepCycle: final / Resolution: 1.99→21.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9108 0 228 959 10295
Biso mean--20.46 30.26 -
Num. residues----1146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0139627
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178917
X-RAY DIFFRACTIONr_angle_refined_deg1.2731.65313042
X-RAY DIFFRACTIONr_angle_other_deg1.1941.58820753
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.41451152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.27222.653475
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.248151648
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8611552
X-RAY DIFFRACTIONr_chiral_restr0.0610.21211
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210887
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021957
LS refinement shellResolution: 1.99→2.042 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 348 -
Rwork0.283 6688 -
all-7036 -
obs--99.03 %
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)
14.4184-5.8499-2.697611.16334.05782.0036-0.1880.1097-0.69140.3127-0.07040.46750.35980.06190.25840.3194-0.0285-0.03880.27180.03040.369410.6383-17.9861-57.9875
23.7258-1.2389-1.12242.45030.5343.03610.14070.2427-0.4866-0.0807-0.08720.27530.3436-0.1368-0.05340.1733-0.077-0.0670.15050.01080.168714.2071-11.2762-62.4864
34.8693-1.6957-0.08624.0407-0.77111.39180.14070.4191-0.2746-0.2654-0.02830.36580.3261-0.1221-0.11240.2107-0.04-0.06680.1944-0.010.096414.636-8.4971-68.513
42.37530.91430.14083.76240.30372.08440.12480.3632-0.1327-0.2635-0.00630.13980.3591-0.0442-0.11850.13470.0389-0.05230.20170.01090.046634.6584-8.0861-61.2312
53.24381.52051.18065.06932.073.6744-0.00220.2264-0.246-0.33130.2626-0.33740.34580.5032-0.26040.1890.0919-0.01990.2315-0.02530.084842.7522-12.9867-60.6665
62.35380.2194-0.14152.7176-0.01061.59210.0747-0.0263-0.11730.09980.0422-0.09550.23930.2089-0.11680.09310.0393-0.04790.1713-0.00970.028638.8136-7.8682-52.4982
71.63640.0113-0.03060.5072-0.12791.1628-0.0025-0.11260.04690.04360.04910.0332-0.0598-0.0476-0.04660.0363-0.0101-0.00190.10680.02050.00922.159312.7087-49.0405
83.3168-0.06940.66241.14310.50622.9246-0.03610.20420.007-0.06610.0326-0.1822-0.01430.36260.00350.082-0.00710.01320.15610.01030.032239.836312.3093-73.8761
95.07852.67696.63844.60311.162710.3971-0.2899-0.11340.705-0.0253-0.28680.7587-0.48260.01990.57670.37850.0650.01520.1609-0.03280.5346-20.108921.9279-14.3534
105.14392.43994.73133.39481.76884.5188-0.13360.00540.4642-0.0325-0.07890.4952-0.1838-0.01320.21240.15040.11910.12850.16720.02030.3523-20.20469.4517-13.6996
112.42960.213-0.78550.39760.0410.98590.1424-0.42110.53830.0889-0.02220.2302-0.39010.0374-0.12020.25060.00420.05740.213-0.08680.2117-9.784111.8644-6.7496
123.28380.54290.00816.42330.38661.364-0.111-0.39160.40290.37220.3049-0.5703-0.21410.5206-0.19390.1764-0.0755-0.0180.3259-0.09270.172812.649210.9976-11.8048
133.14530.1431-0.46662.39550.74840.70190.1192-0.13120.25450.15230.0392-0.0293-0.17140.1699-0.15830.136-0.05740.05650.16790.00210.08094.1627.4092-16.7581
145.6799-2.6999-1.06034.43992.17962.92190.1150.09130.4761-0.19730.08070.0315-0.4150.2353-0.19570.1843-0.07830.04970.20920.02460.121411.207713.3554-23.3709
152.01280.2090.32010.6698-0.05621.7720.07370.1456-0.0182-0.0279-0.00950.06350.0491-0.0761-0.06420.03260.0335-0.00530.09030.0070.0097-15.3374-8.9341-24.5276
161.0569-0.3591-0.1670.26410.12163.50140.07950.0113-0.13630.013-0.0724-0.04880.22280.3624-0.0070.07950.026-0.01910.14910.02940.0967.3859-15.261-10.9811
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 21
2X-RAY DIFFRACTION2A22 - 51
3X-RAY DIFFRACTION3A52 - 74
4X-RAY DIFFRACTION4A75 - 93
5X-RAY DIFFRACTION5A94 - 121
6X-RAY DIFFRACTION6A122 - 160
7X-RAY DIFFRACTION7B3 - 326
8X-RAY DIFFRACTION8B327 - 419
9X-RAY DIFFRACTION9C8 - 14
10X-RAY DIFFRACTION10C15 - 39
11X-RAY DIFFRACTION11C40 - 90
12X-RAY DIFFRACTION12C91 - 118
13X-RAY DIFFRACTION13C119 - 144
14X-RAY DIFFRACTION14C145 - 160
15X-RAY DIFFRACTION15D3 - 236
16X-RAY DIFFRACTION16D237 - 418

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