Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 15.56 kDa 
• Atom Count: 1,176 
• Modelled Residue Count: 135 
• Deposited Residue Count: 135 
• Unique protein chains: 1

 8BRK

Room temperature crystal structure of cytochrome c' from Thermus thermophilus

• PDB DOI:  https://doi.org/10.2210/pdb8BRK/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Thermus thermophilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-11-23 Released: 2023-05-24 
• Deposition Author(s): Fujii, S., Hough, M.A.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.193 
• R-Value Work: 0.158 
• R-Value Observed: 0.160 

Literature

Protein-to-structure pipeline for ambient-temperature in situ crystallography at VMXi.

Mikolajek, H., Sanchez-Weatherby, J., Sandy, J., Gildea, R.J., Campeotto, I., Cheruvara, H., Clarke, J.D., Foster, T., Fujii, S., Paulsen, I.T., Shah, B.S., Hough, M.A.

(2023) IUCrJ 

• PubMed: 37199504 
• DOI: https://doi.org/10.1107/S2052252523003810
• Primary Citation of Related Structures:  
  7ZCK, 8A9D, 8AR6, 8AR9, 8BRK, 8BRL, 8BS8, 8CIF


• PubMed Abstract: 
  

The utility of X-ray crystal structures determined under ambient-temperature conditions is becoming increasingly recognized. Such experiments can allow protein dynamics to be characterized and are particularly well suited to challenging protein targets that may form fragile crystals that are difficult to cryo-cool. Room-temperature data collection also enables time-resolved experiments. In contrast to the high-throughput highly automated pipelines for determination of structures at cryogenic temperatures widely available at synchrotron beamlines, room-temperature methodology is less mature. Here, the current status of the fully automated ambient-temperature beamline VMXi at Diamond Light Source is described, and a highly efficient pipeline from protein sample to final multi-crystal data analysis and structure determination is shown. The capability of the pipeline is illustrated using a range of user case studies representing different challenges, and from high and lower symmetry space groups and varied crystal sizes. It is also demonstrated that very rapid structure determination from crystals in situ within crystallization plates is now routine with minimal user intervention.

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Organizational Affiliation: 

Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable cytochrome	A	135	Thermus thermophilus	Mutation(s): 0  Gene Names: TT_P0091
UniProt
Find proteins for Q746G4 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q746G4  Go to UniProtKB:  Q746G4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEC (Subject of Investigation/LOI)	B [auth A]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.193 
• R-Value Work: 0.158 
• R-Value Observed: 0.160 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.535	α = 90
b = 38.986	β = 97.24
c = 41.525	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
xia2.multiplex	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-05-24 
Deposition Author(s): Fujii, S., Hough, M.A.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History  

• Version 1.0: 2023-05-24
  Type: Initial release
  
• Version 1.1: 2023-05-31
  Changes: Database references