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

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Basic information

Entry
Database: PDB / ID: 6koc
TitleX-ray Structure of the proton-pumping cytochrome aa3-600 menaquinol oxidase from Bacillus subtilis complexed with 3-iodo-N-oxo-2-heptyl-4-hydroxyquinoline
Components
  • (AA3-600 quinol oxidase subunit ...) x 2
  • (Quinol oxidase subunit ...) x 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 / respiratory chain complex / oxidative phosphorylation / cytochrome-c oxidase activity / proton transmembrane transporter activity / electron transport coupled proton 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 / respiratory chain complex / oxidative phosphorylation / cytochrome-c oxidase activity / proton transmembrane transporter activity / electron transport coupled proton transport / ATP synthesis coupled electron transport / aerobic respiration / respiratory electron transport chain / oxidoreductase activity / 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-3-iodanyl-1-oxidanyl-quinolin-4-one / Quinol oxidase subunit 3 / Quinol oxidase subunit 1 / 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)
Bacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 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: Quinol oxidase subunit 4,Quinol oxidase subunit 4
G: AA3-600 quinol oxidase subunit IIII
H: Quinol oxidase subunit 4,Quinol oxidase subunit 4
F: Quinol oxidase subunit 2
E: AA3-600 quinol oxidase subunit I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)289,29216
Polymers284,9838
Non-polymers4,3098
Water00
1
A: AA3-600 quinol oxidase subunit I
B: Quinol oxidase subunit 2
C: AA3-600 quinol oxidase subunit IIII
D: Quinol oxidase subunit 4,Quinol oxidase subunit 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,6468
Polymers142,4924
Non-polymers2,1544
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17160 Å2
ΔGint-184 kcal/mol
Surface area45290 Å2
MethodPISA
2
G: AA3-600 quinol oxidase subunit IIII
H: Quinol oxidase subunit 4,Quinol oxidase subunit 4
F: Quinol oxidase subunit 2
E: AA3-600 quinol oxidase subunit I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,6468
Polymers142,4924
Non-polymers2,1544
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17180 Å2
ΔGint-198 kcal/mol
Surface area45000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.930, 162.200, 151.320
Angle α, β, γ (deg.)90.000, 109.760, 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 ... , 2 types, 4 molecules AECG

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


Mass: 73892.789 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 menaquinol oxidase / Cytochrome aa3-600 quinol oxidase subunit III / Quinol ...cytochrome aa3-600 menaquinol oxidase / 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

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Quinol oxidase subunit ... , 2 types, 4 molecules BFDH

#2: Protein Quinol oxidase subunit 2 / cytochrome aa3-600 menaquinol oxidase


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
#4: Protein Quinol oxidase subunit 4,Quinol oxidase subunit 4 / Quinol oxidase aa3-600 / subunit QoxD / Quinol oxidase polypeptide IV


Mass: 12319.210 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria), (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: qoxD, BSU38140, ipa-40d / Production host: Bacillus subtilis (bacteria)
References: UniProt: P34959, 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-IHQ / 2-heptyl-3-iodanyl-1-oxidanyl-quinolin-4-one


Mass: 385.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H20INO2

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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 ANKSAEHSHFPWKHIVGFILSIVLTLLALWVAVYTDLSSSAKLWII (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: 4.62 Å3/Da / Density % sol: 76.6 %
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: 3.8→48.28 Å / Num. obs: 50255 / % possible obs: 98.5 % / Redundancy: 2.6 % / CC1/2: 0.878 / Rmerge(I) obs: 0.22 / Net I/σ(I): 3.4
Reflection shellResolution: 3.8→3.92 Å / Rmerge(I) obs: 1.264 / Num. unique obs: 4597 / CC1/2: 0.382

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.14_3235refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KOB

6kob


Resolution: 3.8→48.27 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.3691 2011 -
Rwork0.3254 --
obs-48159 98.3785 %
Refinement stepCycle: LAST / Resolution: 3.8→48.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17642 0 270 0 17912
LS refinement shellResolution: 3.8001→3.8951 Å
RfactorNum. reflection% reflection
Rfree0.401 --
Rwork0.3855 --
obs-3549 97.5 %
Refinement TLS params.Method: refined / Origin x: -24.7077 Å / Origin y: 5.1896 Å / Origin z: -12.9278 Å
111213212223313233
T0.6774 Å20.1906 Å20.2448 Å2-0.1263 Å2-0.2241 Å2--0.361 Å2
L1.5186 °2-0.0248 °21.9109 °2-0.9274 °2-0.3283 °2--4.7051 °2
S-0.1224 Å °0.0308 Å °0.018 Å °0.2075 Å °-0.0772 Å °0.0082 Å °-0.3988 Å °-0.0533 Å °0.1531 Å °
Refinement TLS groupSelection details: all

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