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

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Basic information

Entry
Database: PDB / ID: 8ajz
TitleSerial femtosecond crystallography structure of CO bound ba3- type cytochrome c oxidase at 2 milliseconds after irradiation by a 532 nm laser
Components
  • (Cytochrome c oxidase subunit ...) x 2
  • Cytochrome c oxidase polypeptide IIA
KeywordsELECTRON TRANSPORT / Membrane protein / bioenergetics / lipidic cubic phase crystallization / serial femtosecond crystallography / pump- probe method
Function / homology
Function and homology information


cytochrome-c oxidase / oxidative phosphorylation / cytochrome-c oxidase activity / membrane => GO:0016020 / : / 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 IIA / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 2
Similarity search - Component
Biological speciesThermus thermophilus (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. / Bosman, R. / Dahl, P. / Nango, E. / Tanaka, R. ...Safari, C. / Ghosh, S. / Andersson, R. / Johannesson, J. / Donoso, A.V. / Bath, P. / Bosman, R. / Dahl, P. / Nango, E. / Tanaka, R. / Zoric, D. / Svensson, E. / Nakane, T. / Iwata, S. / Neutze, R. / Branden, G.
Funding support Sweden, European Union, 6items
OrganizationGrant numberCountry
Swedish Research Council2017-06734 Sweden
The Swedish Foundation for Strategic Research17-0060 Sweden
Carl Trygger Foundation16:79 Sweden
European Union (EU)789030European Union
Swedish Research Council2015-00560 Sweden
H2020 Marie Curie Actions of the European CommissionX-probeEuropean Union
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 29, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / pdbx_validate_chiral
Item: _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_atom.pdbx_stereo_config ..._chem_comp_atom.pdbx_aromatic_flag / _chem_comp_atom.pdbx_stereo_config / _chem_comp_bond.pdbx_aromatic_flag / _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 IIA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,99523
Polymers85,8913
Non-polymers7,10420
Water3,279182
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)145.85, 100.32, 96.62
Angle α, β, γ (deg.)90, 126.76, 90
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-707-

HOH

21B-369-

HOH

31B-374-

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 (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 (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 IIA / Cytchrome c oxidase subunit 3


Mass: 3769.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: HGMM_F04D06C07, TTMY_0198 / Production host: Thermus thermophilus HB8 (bacteria) / References: UniProt: A0A1J1EEV7

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Non-polymers , 7 types, 202 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.: 182 / 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: 3.39 Å3/Da / Density % sol: 63.71 %
Crystal growTemperature: 298 K / Method: lipidic cubic phase / pH: 5.3
Details: 100 mM 2-Morpholinoethanesulfonic acid, 34-38 % PEG 400 (v/v), 1.4 M NaCl, pH 5.3

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.66 Å
DetectorType: MPCCD / Detector: CCD / Date: Feb 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.66 Å / Relative weight: 1
ReflectionResolution: 2→43.4 Å / Num. obs: 75202 / % possible obs: 100 % / Redundancy: 94.5 % / Biso Wilson estimate: 40.03 Å2 / CC1/2: 0.91 / Net I/σ(I): 3.97
Reflection shellResolution: 2→2.071 Å / Mean I/σ(I) obs: 1.43 / Num. unique obs: 7465 / CC1/2: 0.55
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NDC

5ndc


Resolution: 2→38.7 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.21 --
Rwork0.19 --
obs-75184 99.94 %
Refinement stepCycle: LAST / Resolution: 2→38.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5910 0 386 182 6478

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