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- PDB-6koe: X-ray Structure of the proton-pumping cytochrome aa3-600 menaquin... -

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Basic information

Entry
Database: PDB / ID: 6koe
TitleX-ray Structure of the proton-pumping cytochrome aa3-600 menaquinol oxidase from Bacillus subtilis
Components
  • (AA3-600 quinol oxidase subunit ...) x 3
  • Quinol oxidase subunit 2
KeywordsOXIDOREDUCTASE / Menaquinol oxidase / Complex / Proton pumping / inhibitor
Function / homology
Function and homology information


Oxidoreductases; Acting on diphenols and related substances as donors; With oxygen as acceptor / cytochrome o ubiquinol oxidase complex / cytochrome bo3 ubiquinol oxidase activity / aerobic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / oxidative phosphorylation / cytochrome-c oxidase activity / electron transport coupled proton transport / proton transmembrane transporter activity / ATP synthesis coupled electron transport ...Oxidoreductases; Acting on diphenols and related substances as donors; With oxygen as acceptor / cytochrome o ubiquinol oxidase complex / cytochrome bo3 ubiquinol oxidase activity / aerobic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / oxidative phosphorylation / cytochrome-c oxidase activity / electron transport coupled proton transport / proton transmembrane transporter activity / ATP synthesis coupled electron transport / aerobic respiration / respiratory electron transport chain / membrane raft / copper ion binding / heme binding / plasma membrane
Similarity search - Function
Quinol oxidase subunit II / Quinol oxidase subunit I / Quinol oxidase subunit III / Quinol oxidase subunit IV / : / Ubiquinol oxidase subunit III domain / Cytochrome C oxidase subunit IV, prokaryotes / Prokaryotic Cytochrome C oxidase subunit IV / Cytochrome o ubiquinol oxidase subunit II / Ubiquinol oxidase subunit 2, cupredoxin domain ...Quinol oxidase subunit II / Quinol oxidase subunit I / Quinol oxidase subunit III / Quinol oxidase subunit IV / : / Ubiquinol oxidase subunit III domain / Cytochrome C oxidase subunit IV, prokaryotes / Prokaryotic Cytochrome C oxidase subunit IV / Cytochrome o ubiquinol oxidase subunit II / Ubiquinol oxidase subunit 2, cupredoxin domain / Cytochrome c oxidase, subunit III, four-helix bundle / Cytochrome C Oxidase; Chain A / Cytochrome c oxidase-like, subunit I domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit III-like / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase subunit III / Heme-copper oxidase subunit III family profile. / Cytochrome c oxidase subunit III-like superfamily / Cytochrome c/quinol oxidase subunit II / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Cupredoxins - blue copper proteins / Cupredoxin / Four Helix Bundle (Hemerythrin (Met), subunit A) / Prokaryotic membrane lipoprotein lipid attachment site profile. / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
COPPER (II) ION / HEME-A / 2-HEPTYL-4-HYDROXY QUINOLINE N-OXIDE / Quinol oxidase subunit 3 / Quinol oxidase subunit 1 / Quinol oxidase subunit 4 / Quinol oxidase subunit 2 / Quinol oxidase subunit 1 / Quinol oxidase subunit 2 / Quinol oxidase subunit 3 / Quinol oxidase subunit 4
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.75 Å
AuthorsXu, J. / Ding, Z. / Liu, B. / Li, J. / Gennis, R.B. / Zhu, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Structure of the cytochromeaa3-600 heme-copper menaquinol oxidase bound to inhibitor HQNO shows TM0 is part of the quinol binding site.
Authors: Xu, J. / Ding, Z. / Liu, B. / Yi, S.M. / Li, J. / Zhang, Z. / Liu, Y. / Li, J. / Liu, L. / Zhou, A. / Gennis, R.B. / Zhu, J.
History
DepositionAug 9, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 29, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Nov 22, 2023Group: 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 / pdbx_validate_chiral
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AA3-600 quinol oxidase subunit I
B: Quinol oxidase subunit 2
C: AA3-600 quinol oxidase subunit IIII
D: AA3-600 quinol oxidase subunit IV
G: AA3-600 quinol oxidase subunit IIII
H: AA3-600 quinol oxidase subunit IV
F: Quinol oxidase subunit 2
E: AA3-600 quinol oxidase subunit I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)290,86816
Polymers286,8118
Non-polymers4,0578
Water00
1
A: AA3-600 quinol oxidase subunit I
B: Quinol oxidase subunit 2
C: AA3-600 quinol oxidase subunit IIII
D: AA3-600 quinol oxidase subunit IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,4348
Polymers143,4064
Non-polymers2,0294
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17640 Å2
ΔGint-188 kcal/mol
Surface area45480 Å2
MethodPISA
2
G: AA3-600 quinol oxidase subunit IIII
H: AA3-600 quinol oxidase subunit IV
F: Quinol oxidase subunit 2
E: AA3-600 quinol oxidase subunit I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,4348
Polymers143,4064
Non-polymers2,0294
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17680 Å2
ΔGint-196 kcal/mol
Surface area44920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.988, 162.110, 149.509
Angle α, β, γ (deg.)90.000, 109.020, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

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AA3-600 quinol oxidase subunit ... , 3 types, 6 molecules AECGDH

#1: Protein AA3-600 quinol oxidase subunit I / Cytochrome aa3 quinol oxidase subunit I / Cytochrome aa3-600 quinol oxidase subunit I


Mass: 74721.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria)
Gene: qoxB, B4122_4931, B4417_2140, ETA10_20065, ETK61_21170, ETL41_11350, SC09_contig4orf01211
Production host: Bacillus subtilis (bacteria) / References: UniProt: A0A063X8D0, UniProt: P34956*PLUS
#3: Protein AA3-600 quinol oxidase subunit IIII / Cytochrome aa3-600 quinol oxidase subunit III / Quinol oxidase subunit 3


Mass: 22689.572 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria)
Gene: B4122_4930, B4417_2139, ETA10_20060, ETK61_21165, ETL41_11345, SC09_contig4orf01209
Production host: Bacillus subtilis (bacteria) / References: UniProt: A0A063X6N5, UniProt: P34958*PLUS
#4: Protein AA3-600 quinol oxidase subunit IV / Cytochrome aa3-600 quinol oxidase subunit IV / Quinol oxidase subunit 4


Mass: 12404.315 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Production host: Bacillus subtilis (bacteria) / References: UniProt: A0A063XC43, UniProt: P34959*PLUS

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Protein , 1 types, 2 molecules BF

#2: Protein Quinol oxidase subunit 2


Mass: 33589.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: qoxA, ETA10_20070, ETK61_21175, ETL41_11355 / Production host: Bacillus subtilis (bacteria)
References: UniProt: A0A2I7T8S1, UniProt: P34957*PLUS, Oxidoreductases; Acting on diphenols and related substances as donors; With oxygen as acceptor

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Non-polymers , 3 types, 8 molecules

#5: Chemical
ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C49H56FeN4O6
#6: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#7: Chemical ChemComp-HQO / 2-HEPTYL-4-HYDROXY QUINOLINE N-OXIDE / 2-HEPTYL-1-OXY-QUINOLIN-4-OL


Mass: 259.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H21NO2

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Details

Has ligand of interestN
Sequence detailsAuthors know the sequence of chain D/H, but they are not sure of the alignment for first 22 ...Authors know the sequence of chain D/H, but they are not sure of the alignment for first 22 residues in the coordinates. The residue numbers 0-21 in the coordinates may be meaningless. The correct sequence is MANKSAEHSHFPWKHIVGFILSIVLTLLALWVAVYTDLSSSAKLWII (UNP P34959)

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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: 4.5 Å3/Da / Density % sol: 76.21 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 0.1 M Calcium chloride, 0.1M Tris pH 6.3, 13% PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.75→49.252 Å / Num. obs: 52047 / % possible obs: 99.5 % / Redundancy: 3 % / CC1/2: 0.854 / Rmerge(I) obs: 0.227 / Net I/σ(I): 3.9
Reflection shellResolution: 3.75→3.87 Å / Rmerge(I) obs: 1.337 / Num. unique obs: 4517 / CC1/2: 0.437

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.14_3235refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KOC

3koc


Resolution: 3.75→49.252 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.3681 1993 -
Rwork0.3469 --
obs-50010 99.5 %
Refinement stepCycle: LAST / Resolution: 3.75→49.252 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17642 0 268 0 17910
LS refinement shellResolution: 3.7501→3.8438 Å
RfactorNum. reflection% reflection
Rfree0.4215 --
Rwork0.4184 --
obs-3676 99 %
Refinement TLS params.Method: refined / Origin x: -24.7074 Å / Origin y: 4.8848 Å / Origin z: -12.8379 Å
111213212223313233
T0.497 Å20.0546 Å20.317 Å2-0.1866 Å2-0.1661 Å2--0.5588 Å2
L1.9165 °2-0.1771 °22.9254 °2-0.8945 °2-0.6421 °2--6.5817 °2
S-0.1549 Å °0.1563 Å °0.0548 Å °0.1072 Å °-0.137 Å °-0.0083 Å °-0.5033 Å °0.1312 Å °0.1324 Å °
Refinement TLS groupSelection details: all

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