Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 22.38 kDa 
• Atom Count: 1673 
• Modelled Residue Count: 207 
• Deposited Residue Count: 207 
• Unique protein chains: 1

6SRO

X-ray pump X-ray probe on thaumatin nanocrystals: 76 fs time delay

• PDB DOI: 10.2210/pdb6SRO/pdb

• Classification: PLANT PROTEIN
• Organism(s): Thaumatococcus daniellii
• Mutation(s): No 


• Deposited: 2019-09-05 Released: 2020-04-22 
• Deposition Author(s): Kloos, M., Gorel, A., Nass, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.177 
• R-Value Work: 0.145 
• R-Value Observed: 0.147 

Literature

Structural dynamics in proteins induced by and probed with X-ray free-electron laser pulses.

Nass, K., Gorel, A., Abdullah, M.M., V Martin, A., Kloos, M., Marinelli, A., Aquila, A., Barends, T.R.M., Decker, F.J., Bruce Doak, R., Foucar, L., Hartmann, E., Hilpert, M., Hunter, M.S., Jurek, Z., Koglin, J.E., Kozlov, A., Lutman, A.A., Kovacs, G.N., Roome, C.M., Shoeman, R.L., Santra, R., Quiney, H.M., Ziaja, B., Boutet, S., Schlichting, I.

(2020) Nat Commun 11: 1814-1814

• PubMed: 32286284 
• DOI: 10.1038/s41467-020-15610-4
• Primary Citation of Related Structures:  
  6SR0, 6SR1, 6SR2, 6SR3, 6SR4, 6SR5, 6SRJ, 6SRK, 6SRL, 6SRO, 6SRP, 6SRQ


• PubMed Abstract: 
  

X-ray free-electron lasers (XFELs) enable crystallographic structure determination beyond the limitations imposed upon synchrotron measurements by radiation damage. The need for very short XFEL pulses is relieved through gating of Bragg diffraction by loss of crystalline order as damage progresses, but not if ionization events are spatially non-uniform due to underlying elemental distributions, as in biological samples. Indeed, correlated movements of iron and sulfur ions were observed in XFEL-irradiated ferredoxin microcrystals using unusually long pulses of 80 fs. Here, we report a femtosecond time-resolved X-ray pump/X-ray probe experiment on protein nanocrystals. We observe changes in the protein backbone and aromatic residues as well as disulfide bridges. Simulations show that the latter's correlated structural dynamics are much slower than expected for the predicted high atomic charge states due to significant impact of ion caging and plasma electron screening. This indicates that dense-environment effects can strongly affect local radiation damage-induced structural dynamics.

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Organizational Affiliation: 

Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thaumatin-1	A	207	Thaumatococcus daniellii	Mutation(s): 0
UniProt
Find proteins for P02883 (Thaumatococcus daniellii) Explore P02883  Go to UniProtKB:  P02883

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TLA	B [auth A]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.177 
• R-Value Work: 0.145 
• R-Value Observed: 0.147 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.849	α = 90
b = 57.849	β = 90
c = 150.328	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystFEL	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2019-09-05 
• Released Date: 2020-04-22 
Deposition Author(s): Kloos, M., Gorel, A., Nass, K.

Revision History  

• Version 1.0: 2020-04-22
  Type: Initial release