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- PDB-8k65: Serial femtosecond crystallography structure of CO bound ba3- typ... -

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Basic information

Entry
Database: PDB / ID: 8k65
TitleSerial femtosecond crystallography structure of CO bound ba3- type cytochrome c oxidase without pump laser irradiation
Components
  • (Cytochrome c oxidase subunit ...) x 2
  • Cytochrome c oxidase polypeptide 2A
KeywordsELECTRON TRANSPORT / Membrane proteins / structural dynamics / serial femtosecond crystallography / time-resolved studies
Function / homology
Function and homology information


cytochrome-c oxidase / oxidative phosphorylation / cytochrome-c oxidase activity / : / copper ion binding / heme binding / metal ion binding / plasma membrane
Similarity search - Function
Cytochrome c oxidase polypeptide 2A / Cytochrome c oxidase polypeptide 2A, ba3 type / Cytochrome c oxidase subunit IIa family / Ba3-like heme-copper oxidase subunit I / Cytochrome C oxidase subunit IIa, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane / Ba3-like heme-copper oxidase subunit II, C-terminal / : / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. ...Cytochrome c oxidase polypeptide 2A / Cytochrome c oxidase polypeptide 2A, ba3 type / Cytochrome c oxidase subunit IIa family / Ba3-like heme-copper oxidase subunit I / Cytochrome C oxidase subunit IIa, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane / Ba3-like heme-copper oxidase subunit II, C-terminal / : / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / 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. / Cupredoxin
Similarity search - Domain/homology
CARBON MONOXIDE / COPPER (II) ION / DINUCLEAR COPPER ION / HEME-AS / PROTOPORPHYRIN IX CONTAINING FE / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Cytochrome c oxidase polypeptide 2A / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 2
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSafari, C. / Ghosh, S. / Andersson, R. / Johannesson, J. / Donoso, A.V. / Bath, P. / Zoric, D. / Sandelin, E. / Nango, E. / Tanaka, R. ...Safari, C. / Ghosh, S. / Andersson, R. / Johannesson, J. / Donoso, A.V. / Bath, P. / Zoric, D. / Sandelin, E. / Nango, E. / Tanaka, R. / Iwata, S. / Neutze, R. / Branden, G.
Funding support Sweden, European Union, Japan, 6items
OrganizationGrant numberCountry
Swedish Research Council2017-06734 and 2021-05662 Sweden
Carl Trygger FoundationCTS 16:79 Sweden
European Research Council (ERC)789030European Union
Swedish Research Council2015-00560 Sweden
European CommissionMarie Curie Training Network X-probeEuropean Union
Japan Agency for Medical Research and Development (AMED)JP21am0101070 Japan
CitationJournal: Sci Adv / Year: 2023
Title: Time-resolved serial crystallography to track the dynamics of carbon monoxide in the active site of cytochrome c oxidase.
Authors: Safari, C. / Ghosh, S. / Andersson, R. / Johannesson, J. / Bath, P. / Uwangue, O. / Dahl, P. / Zoric, D. / Sandelin, E. / Vallejos, A. / Nango, E. / Tanaka, R. / Bosman, R. / Borjesson, P. / ...Authors: Safari, C. / Ghosh, S. / Andersson, R. / Johannesson, J. / Bath, P. / Uwangue, O. / Dahl, P. / Zoric, D. / Sandelin, E. / Vallejos, A. / Nango, E. / Tanaka, R. / Bosman, R. / Borjesson, P. / Dunevall, E. / Hammarin, G. / Ortolani, G. / Panman, M. / Tanaka, T. / Yamashita, A. / Arima, T. / Sugahara, M. / Suzuki, M. / Masuda, T. / Takeda, H. / Yamagiwa, R. / Oda, K. / Fukuda, M. / Tosha, T. / Naitow, H. / Owada, S. / Tono, K. / Nureki, O. / Iwata, S. / Neutze, R. / Branden, G.
History
DepositionJul 25, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c oxidase subunit 1
B: Cytochrome c oxidase subunit 2
C: Cytochrome c oxidase polypeptide 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,99523
Polymers85,8913
Non-polymers7,10420
Water3,423190
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.850, 100.320, 96.620
Angle α, β, γ (deg.)90.000, 126.760, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-748-

HOH

21B-373-

HOH

31B-376-

HOH

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Components

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Cytochrome c oxidase subunit ... , 2 types, 2 molecules AB

#1: Protein Cytochrome c oxidase subunit 1 / Cytochrome c ba(3) subunit I / Cytochrome c oxidase polypeptide I / Cytochrome cba3 subunit 1


Mass: 63540.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: cbaA, TTHA1135 / Production host: Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SJ79, cytochrome-c oxidase
#2: Protein Cytochrome c oxidase subunit 2 / Cytochrome c ba(3) subunit II / Cytochrome c oxidase polypeptide II / Cytochrome cba3 subunit 2


Mass: 18581.299 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: cbaB, ctaC, TTHA1134 / Production host: Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SJ80, cytochrome-c oxidase

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Cytochrome c oxidase polypeptide 2A / Cytochrome c ba(3) subunit IIA / Cytochrome c oxidase polypeptide IIA / Cytochrome cba3 subunit 2A


Mass: 3769.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: cbaD, TTHA1133 / Production host: Thermus thermophilus HB8 (bacteria) / References: UniProt: P82543, cytochrome-c oxidase

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Non-polymers , 7 types, 210 molecules

#4: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-HAS / HEME-AS


Mass: 920.954 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C54H64FeN4O6 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C21H40O4 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu2 / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.3 Å3/Da / Density % sol: 62.69 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.3 / Details: 34-38 % PEG 400 (v/v), 1.4 M NaCl, pH 5.3

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 0.987 Å
DetectorType: MPCCD / Detector: CCD / Date: Feb 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2→43.4 Å / Num. obs: 75223 / % possible obs: 100 % / Redundancy: 233.9 % / CC1/2: 0.95 / Net I/σ(I): 5.4
Reflection shellResolution: 2→2.1 Å / Num. unique obs: 7471 / CC1/2: 0.466

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Processing

Software
NameVersionClassification
REFMACv8.0refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→37.2 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.92 / SU ML: 0 / Cross valid method: FREE R-VALUE / ESU R: 0.129 / ESU R Free: 0.142
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.196 3773 5.017 %
Rwork0.17 71438 -
all0.211 --
obs-75208 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 37.834 Å2
Baniso -1Baniso -2Baniso -3
1--0.119 Å20 Å20.661 Å2
2---1.133 Å20 Å2
3---0.125 Å2
Refinement stepCycle: LAST / Resolution: 2→37.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5910 0 386 190 6486
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0520.8572590.7945284X-RAY DIFFRACTION100
2.052-2.1080.492470.5125115X-RAY DIFFRACTION100
2.108-2.1690.3272450.3074988X-RAY DIFFRACTION100
2.169-2.2350.2322570.1934847X-RAY DIFFRACTION100
2.235-2.3080.1912480.1614657X-RAY DIFFRACTION100
2.308-2.3890.1982280.1534614X-RAY DIFFRACTION100
2.389-2.4790.1742490.1554323X-RAY DIFFRACTION100
2.479-2.580.1762390.1624225X-RAY DIFFRACTION100
2.58-2.6940.2042070.174033X-RAY DIFFRACTION100
2.694-2.8250.1921880.1713890X-RAY DIFFRACTION100
2.825-2.9770.1911900.1753689X-RAY DIFFRACTION100
2.977-3.1560.211860.1743512X-RAY DIFFRACTION100
3.156-3.3720.2161670.183269X-RAY DIFFRACTION100
3.372-3.640.1921910.1773051X-RAY DIFFRACTION100
3.64-3.9840.1921370.1652828X-RAY DIFFRACTION100
3.984-4.4490.1921660.1712547X-RAY DIFFRACTION100
4.449-5.1250.2241270.1972250X-RAY DIFFRACTION100
5.125-6.250.1991130.2051925X-RAY DIFFRACTION100
6.25-8.7260.318770.2921512X-RAY DIFFRACTION100
8.726-37.20.571520.601879X-RAY DIFFRACTION99.148

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