RCSB PDB - 8HUA: Serial synchrotron crystallography structure of ba3-type cytochrome c oxidase from Thermus thermophilus using a goniometer compatible flow-cell

 8HUA

Serial synchrotron crystallography structure of ba3-type cytochrome c oxidase from Thermus thermophilus using a goniometer compatible flow-cell


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.152 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HASClick on this verticalbar to view detailsBest fitted HEMClick on this verticalbar to view detailsBest fitted OLCClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

A simple goniometer-compatible flow cell for serial synchrotron X-ray crystallography.

Ghosh, S.Zoric, D.Dahl, P.Bjelcic, M.Johannesson, J.Sandelin, E.Borjesson, P.Bjorling, A.Banacore, A.Edlund, P.Aurelius, O.Milas, M.Nan, J.Shilova, A.Gonzalez, A.Mueller, U.Branden, G.Neutze, R.

(2023) J Appl Crystallogr 56: 449-460

  • DOI: https://doi.org/10.1107/S1600576723001036
  • Primary Citation of Related Structures:  
    8HUA

  • PubMed Abstract: 

    Serial femtosecond crystallography was initially developed for room-temperature X-ray diffraction studies of macromolecules at X-ray free electron lasers. When combined with tools that initiate biological reactions within microcrystals, time-resolved serial crystallography allows the study of structural changes that occur during an enzyme catalytic reaction. Serial synchrotron X-ray crystallography (SSX), which extends serial crystallography methods to synchrotron radiation sources, is expanding the scientific community using serial diffraction methods. This report presents a simple flow cell that can be used to deliver microcrystals across an X-ray beam during SSX studies. This device consists of an X-ray transparent glass capillary mounted on a goniometer-compatible 3D-printed support and is connected to a syringe pump via light-weight tubing. This flow cell is easily mounted and aligned, and it is disposable so can be rapidly replaced when blocked. This system was demonstrated by collecting SSX data at MAX IV Laboratory from microcrystals of the integral membrane protein cytochrome c oxidase from Thermus thermophilus , from which an X-ray structure was determined to 2.12 Å resolution. This simple SSX platform may help to lower entry barriers for non-expert users of SSX.


  • Organizational Affiliation

    Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9C, 40530 Gothenburg, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1569Thermus thermophilusMutation(s): 0 
Gene Names: cbaATTHA1135
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
Find proteins for Q5SJ79 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SJ79 
Go to UniProtKB:  Q5SJ79
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SJ79
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2168Thermus thermophilus HB8Mutation(s): 0 
Gene Names: cbaBctaCTTHA1134
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
Find proteins for Q5SJ80 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SJ80 
Go to UniProtKB:  Q5SJ80
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SJ80
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide 2A34Thermus thermophilus HB8Mutation(s): 0 
Gene Names: cbaDTTHA1133
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
Find proteins for P82543 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P82543 
Go to UniProtKB:  P82543
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP82543
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HAS (Subject of Investigation/LOI)
Query on HAS

Download Ideal Coordinates CCD File 
F [auth A]HEME-AS
C54 H64 Fe N4 O6
PDYODZVCODUKFH-ZOMLSHGTSA-L
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
E [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
OLC (Subject of Investigation/LOI)
Query on OLC

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
CUA (Subject of Investigation/LOI)
Query on CUA

Download Ideal Coordinates CCD File 
R [auth B]DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
CU (Subject of Investigation/LOI)
Query on CU

Download Ideal Coordinates CCD File 
D [auth A]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.152 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.06α = 90
b = 100.17β = 126.76
c = 96.62γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HASClick on this verticalbar to view detailsBest fitted HEMClick on this verticalbar to view detailsBest fitted OLCClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2015-00560
European Union (EU)European Union789030
European Union (EU)European Union963936
The Swedish Foundation for Strategic ResearchSweden17-0060
Swedish Research CouncilSweden2017-06734
Swedish Research CouncilSweden2021-05662

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-01
    Type: Initial release
  • Version 1.1: 2023-04-26
    Changes: Database references
  • Version 1.2: 2024-05-29
    Changes: Data collection, Source and taxonomy