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- PDB-6r7p: Crystal structure of oxidized Aquifex aeolicus NADH-quinone oxido... -

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Basic information

Entry
Database: PDB / ID: 6r7p
TitleCrystal structure of oxidized Aquifex aeolicus NADH-quinone oxidoreductase subunits NuoE and NuoF S96M
Components(NADH-quinone oxidoreductase subunit ...NADH dehydrogenase (quinone)) x 2
KeywordsOXIDOREDUCTASE / respiratory chain / complex I / NADH ubiquinone oxidoreductase / Fe-S clusters
Function / homology
Function and homology information


plasma membrane respiratory chain complex I / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / 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. / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NuoE domain / NADH-quinone oxidoreductase subunit E-like / Thioredoxin-like [2Fe-2S] ferredoxin / NADH-quinone oxidoreductase subunit E, N-terminal ...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. / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NuoE domain / NADH-quinone oxidoreductase subunit E-like / Thioredoxin-like [2Fe-2S] ferredoxin / NADH-quinone oxidoreductase subunit E, N-terminal / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Respiratory-chain NADH dehydrogenase 51 Kd subunit / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / 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 (bacteria)
Aquifex aeolicus VF5 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.22 Å
AuthorsWohlwend, D. / 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
DepositionMar 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)136,59417
Polymers134,2824
Non-polymers2,31213
Water2,000111
1
A: NADH-quinone oxidoreductase subunit E
B: NADH-quinone oxidoreductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3759
Polymers67,1412
Non-polymers1,2347
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: NADH-quinone oxidoreductase subunit E
D: NADH-quinone oxidoreductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2198
Polymers67,1412
Non-polymers1,0786
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.410, 114.640, 187.870
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 (quinone) / 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 (bacteria) / Gene: nuoE, aq_574 / Plasmid: pETBlue-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2
References: UniProt: O66842, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#2: Protein NADH-quinone oxidoreductase subunit F / NADH dehydrogenase (quinone) / NADH dehydrogenase I subunit F / NDH-1 subunit F


Mass: 48567.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Gene: nuoF, aq_573 / Plasmid: pETBlue-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2
References: UniProt: O66841, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions

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Non-polymers , 7 types, 124 molecules

#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


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


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.64 Å3/Da / Density % sol: 53.32 % / Mosaicity: 0.57 °
Crystal growTemperature: 289 K / Method: evaporation / pH: 6.5
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: Mar 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 3.22→38.21 Å / Num. obs: 22909 / % possible obs: 99.8 % / Redundancy: 6.7 % / CC1/2: 0.991 / Rmerge(I) obs: 0.269 / Rpim(I) all: 0.11 / Rrim(I) all: 0.291 / Net I/σ(I): 6.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.22-3.486.80.8946550.7950.3670.964100
8.52-38.215.10.04513050.9990.020.04996.2

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Processing

Software
NameVersionClassification
MOSFLM7.2.1data reduction
Aimless0.7.4data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.24data extraction
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Q9K

6q9k


Resolution: 3.22→31.73 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.907 / SU B: 57.764 / SU ML: 0.471 / SU R Cruickshank DPI: 0.4746 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.554
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2572 1112 4.9 %RANDOM
Rwork0.2079 ---
obs0.2104 21749 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 172.8 Å2 / Biso mean: 60.227 Å2 / Biso min: 5.47 Å2
Baniso -1Baniso -2Baniso -3
1--1.66 Å20 Å2-0 Å2
2--2.43 Å20 Å2
3----0.77 Å2
Refinement stepCycle: final / Resolution: 3.22→31.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9104 0 101 111 9316
Biso mean--68.39 32.15 -
Num. residues----1146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0139517
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178860
X-RAY DIFFRACTIONr_angle_refined_deg1.3211.64912889
X-RAY DIFFRACTIONr_angle_other_deg1.1211.58120613
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.67351156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.80722.72478
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.177151649
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9141552
X-RAY DIFFRACTIONr_chiral_restr0.0530.21195
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210728
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021948
LS refinement shellResolution: 3.22→3.303 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 77 -
Rwork0.325 1576 -
all-1653 -
obs--99.88 %
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)
112.612-10.216-3.07039.43970.65693.9059-0.08750.3332-0.5546-0.2719-0.09020.13320.4816-0.19840.17770.6962-0.19820.04020.4637-0.2650.883611.2642-18.5546-58.1359
20.4894-1.775-0.90511.84343.21191.9309-0.19670.3981-0.4040.0276-0.28140.71760.6869-0.74850.4780.5985-0.2325-0.06130.6896-0.44490.754914.6818-11.311-61.9919
31.6526-1.02761.796611.1936-0.1432.29550.50560.3767-0.0923-0.613-0.61780.58160.4903-0.02270.11210.5278-0.0348-0.08740.8281-0.26730.134314.8557-8.3293-68.0809
40.2687-0.618-0.757510.46860.28042.676-0.15270.05910.0252-0.52880.3873-0.6730.63740.0961-0.23460.23230.07630.0120.5839-0.23880.315235.1573-7.4005-60.7811
57.933-0.87410.89818.03476.95596.84090.06040.7274-0.4443-0.72160.4299-0.6801-0.1520.7754-0.49030.61660.19720.20720.4448-0.02980.257843.2276-12.0693-60.4088
66.71490.7522-0.17276.6731-0.87584.65520.01520.1096-0.08950.1458-0.0096-0.14180.09550.2846-0.00570.27380.0803-0.02520.12120.00360.007539.0588-7.3041-52.0691
75.07550.57610.59951.44760.151.7713-0.02390.26990.419-0.16490.15040.1202-0.2123-0.0036-0.12660.2796-0.03070.00310.0820.08180.100321.906512.5986-47.9722
84.96530.06230.18912.84540.15475.0544-0.05730.9839-0.1647-0.425-0.098-0.12640.03660.4510.15540.6686-0.05830.04350.9020.07690.51939.795813.2774-72.5102
95.26672.479712.490912.06141.610131.3588-0.1906-0.31440.33490.3055-0.65050.0569-0.4883-0.6650.84110.630.0190.02730.4497-0.09890.7074-19.5221.6917-13.7045
101.2061-0.98991.47127.33921.53342.99-0.126-0.38940.3242-0.2301-0.44740.4423-0.3721-0.74350.57340.530.05950.12560.5372-0.26770.4596-20.0258.9984-13.0676
113.35930.1111-2.44530.92981.56164.88840.2835-1.52650.74080.0373-0.36420.4232-0.4650.36230.08070.59420.10730.12691.0194-0.32480.479-9.638611.1532-5.9079
125.47425.23180.78689.5017-1.39611.2334-0.2596-0.4123-0.15610.580.063-0.8644-0.5142-0.02550.19650.4462-0.134-0.03210.7579-0.370.282212.8039.8077-10.9246
137.7108-1.9531.70681.8868-1.52861.29640.1466-0.57760.19610.3034-0.12420.1208-0.250.1537-0.02240.3536-0.11770.09950.291-0.06660.18414.22526.4458-15.9135
1410.5013-4.7008-3.5384.6623-2.95019.25220.5019-0.51310.7962-0.3809-0.0152-0.19380.04050.6016-0.48680.406-0.1356-0.05480.3175-0.06970.355611.357412.3687-22.3897
155.47950.0230.27541.58580.35382.57880.0827-0.2391-0.28740.24020.07460.04410.1185-0.208-0.15730.20650.0316-0.03160.10020.07260.0742-15.5989-9.2857-23.8449
163.0756-0.1184-0.23420.85780.06266.48320.1058-0.8431-0.21950.583-0.1557-0.02930.37440.4460.04990.5630.0206-0.05980.47950.05250.34967.1742-16.2682-10.6742
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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