5FGT | pdb_00005fgt

Thaumatin solved by native sulphur-SAD using free-electron laser radiation

• PDB DOI: https://doi.org/10.2210/pdb5FGT/pdb

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


• Deposited: 2015-12-21 Released: 2016-06-08 
• Deposition Author(s): Nass, K.J., Meinhart, A., Barends, T.R.M., Foucar, L., Gorel, A., Aquila, A., Botha, S., Doak, R.B., Koglin, J., Liang, M., Shoeman, R.L., Williams, G.K., Boutet, S., Schlichting, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.186 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.154 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Literature

Protein structure determination by single-wavelength anomalous diffraction phasing of X-ray free-electron laser data.

Nass, K., Meinhart, A., Barends, T.R., Foucar, L., Gorel, A., Aquila, A., Botha, S., Doak, R.B., Koglin, J., Liang, M., Shoeman, R.L., Williams, G., Boutet, S., Schlichting, I.

(2016) IUCrJ 3: 180-191

• PubMed: 27158504 
• DOI: https://doi.org/10.1107/S2052252516002980
• Primary Citation Related Structures: 
  5FGT, 5FGX


• PubMed Abstract: 
  

  Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) offers unprecedented possibilities for macromolecular structure determination of systems that are prone to radiation damage. However, phasing XFEL data de novo is complicated by the inherent inaccuracy of SFX data, and only a few successful examples, mostly based on exceedingly strong anomalous or isomorphous difference signals, have been reported. Here, it is shown that SFX data from thaumatin microcrystals can be successfully phased using only the weak anomalous scattering from the endogenous S atoms. Moreover, a step-by-step investigation is presented of the particular problems of SAD phasing of SFX data, analysing data from a derivative with a strong anomalous signal as well as the weak signal from endogenous S atoms.

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Organizational Affiliation: 
• Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research , Jahnstrasse 29, 69120 Heidelberg, Germany.
European XFEL GmbH , Albert-Einstein-Ring 19, 22761 Hamburg, Germany.
SLAC National Accelerator Laboratory , 2575 Sand Hill Road, Menlo Park, CA 94025, USA.

Biological Assembly 1  

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: 1,696 
• Modeled Residue Count: 207 
• Deposited Residue Count: 207 
• Unique protein chains: 1

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: 2.10 Å
• R-Value Free:  0.186 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.154 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.6	α = 90
b = 58.6	β = 90
c = 151.3	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
XSCALE	data scaling
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-06-08 
Deposition Author(s): Nass, K.J., Meinhart, A., Barends, T.R.M., Foucar, L., Gorel, A., Aquila, A., Botha, S., Doak, R.B., Koglin, J., Liang, M., Shoeman, R.L., Williams, G.K., Boutet, S., Schlichting, I.

Revision History  

• Version 1.0: 2016-06-08
  Type: Initial release
  
• Version 1.1: 2018-11-14
  Changes: Data collection
• Version 1.2: 2024-10-23
  Changes: Data collection, Database references, Structure summary