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- PDB-8k6y: Serial femtosecond crystallography structure of photo dissociated... -

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Basic information

Entry
Database: PDB / ID: 8k6y
TitleSerial femtosecond crystallography structure of photo dissociated CO from ba3- type cytochrome c oxidase determined by extrapolation method
Components
  • (Cytochrome c oxidase subunit ...) x 2
  • Cytochrome c oxidase polypeptide 2A
KeywordsELECTRON TRANSPORT / membrane protein / bioenergetics of cells / 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 subunit II, transmembrane domain superfamily ...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. / Zoric, D. / Sandelin, E. / 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
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13720 Å2
ΔGint-153 kcal/mol
Surface area26460 Å2
MethodPISA
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-765-

HOH

21B-334-

HOH

31B-368-

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, 198 molecules

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


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


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#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
#8: Chemical ChemComp-CMO / CARBON MONOXIDE


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


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


Mass: 18.015 Da / Num. of mol.: 178 / 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: 71307 / % possible obs: 94.78 % / Redundancy: 99.1 % / CC1/2: 0.91 / Net I/σ(I): 4
Reflection shellResolution: 2→2.071 Å / Num. unique obs: 6929 / CC1/2: 0.55

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Processing

Software
NameVersionClassification
REFMACv8.0refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→37.151 Å / Cor.coef. Fo:Fc: 0.805 / Cor.coef. Fo:Fc free: 0.754 / SU B: 23.934 / SU ML: 0.63 / Cross valid method: FREE R-VALUE / ESU R: 0.293 / ESU R Free: 0.273 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.4354 1877 2.632 %
Rwork0.3961 69430 -
all0.397 --
obs-71307 94.783 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 36.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.109 Å2-0 Å20.515 Å2
2---0.684 Å20 Å2
3---0.011 Å2
Refinement stepCycle: LAST / Resolution: 2→37.151 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5910 0 386 178 6474
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0126493
X-RAY DIFFRACTIONr_angle_refined_deg1.841.6738845
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6995749
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.649548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.4210890
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.68110228
X-RAY DIFFRACTIONr_chiral_restr0.130.2969
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024927
X-RAY DIFFRACTIONr_nbd_refined0.2440.23014
X-RAY DIFFRACTIONr_nbtor_refined0.3180.24310
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2410.2267
X-RAY DIFFRACTIONr_metal_ion_refined0.1010.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1910.278
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2230.232
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2-2.0520.4911240.6150090.60755410.740.70492.63670.61
2.052-2.1080.6141520.57747000.57853620.5920.65990.48860.574
2.108-2.1690.5181210.51747090.51752330.8080.83192.29890.514
2.169-2.2350.4461180.44546840.44551020.8730.87194.120.445
2.235-2.3080.4951320.40645520.40949070.8380.89295.45550.407
2.308-2.3890.4531150.40445310.40548380.8490.89796.03140.413
2.389-2.4790.4351170.40642870.40745730.8550.89696.30440.418
2.479-2.580.4261040.38442000.38544650.8890.90296.39420.398
2.58-2.6940.4081050.38639790.38642380.8770.90296.36620.404
2.694-2.8240.4621050.39438070.39640740.8760.89696.02360.413
2.824-2.9760.453930.40736240.40838810.8830.89695.77430.439
2.976-3.1550.496950.40734410.40936980.8540.89695.61930.44
3.155-3.3720.431930.4431750.4434320.8890.87995.22150.487
3.372-3.6390.513750.38830250.39132420.8360.90595.620.437
3.639-3.9830.376790.3427530.34129620.9170.92895.61110.385
3.983-4.4460.37680.33525460.33627210.9220.92996.06760.37
4.446-5.1220.359650.31822380.31923750.9150.93496.96840.342
5.122-6.2440.382510.36118670.36120380.9130.91794.11190.402
6.244-8.7080.383380.37314620.37315930.560.72494.1620.404
8.708-37.1510.368270.3138410.3159420.7420.84692.14440.336

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