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: 1563 
• Modelled Residue Count: 207 
• Deposited Residue Count: 207 
• Unique protein chains: 1

6S1D

Structure of thaumatin determined at SwissFEL using native-SAD at 4.57 keV from 20,000 diffraction patterns

• PDB DOI: 10.2210/pdb6S1D/pdb

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


• Deposited: 2019-06-18 Released: 2020-07-15 
• Deposition Author(s): Nass, K., Cheng, R., Vera, L., Mozzanica, A., Redford, S., Ozerov, D., Basu, S., James, D., Knopp, G., Cirelli, C., Martiel, I., Casadei, C., Weinert, T., Nogly, P., Skopintsev, P., Usov, I., Leonarski, F., Geng, T., Rappas, M., Dore, A.S., Cooke, R., Nasrollahi Shirazi, S., Dworkowski, F., Sharpe, M., Olieric, N., Steinmetz, M.O., Schertler, G., Abela, R., Patthey, L., Schmitt, B., Hennig, M., Standfuss, J., Wang, M., Milne, J.C.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.196 
• R-Value Work: 0.153 
• R-Value Observed: 0.155 

Literature

Advances in long-wavelength native phasing at X-ray free-electron lasers.

Nass, K., Cheng, R., Vera, L., Mozzanica, A., Redford, S., Ozerov, D., Basu, S., James, D., Knopp, G., Cirelli, C., Martiel, I., Casadei, C., Weinert, T., Nogly, P., Skopintsev, P., Usov, I., Leonarski, F., Geng, T., Rappas, M., Dore, A.S., Cooke, R., Nasrollahi Shirazi, S., Dworkowski, F., Sharpe, M., Olieric, N., Bacellar, C., Bohinc, R., Steinmetz, M.O., Schertler, G., Abela, R., Patthey, L., Schmitt, B., Hennig, M., Standfuss, J., Wang, M., Milne, C.J.

(2020) IUCrJ 7: 965-975

• PubMed: 33209311 
• DOI: 10.1107/S2052252520011379
• Primary Citation of Related Structures:  
  6S0L, 6S0Q, 6S19, 6S1D, 6S1E, 6S1G


• PubMed Abstract: 
  

Long-wavelength pulses from the Swiss X-ray free-electron laser (XFEL) have been used for de novo protein structure determination by native single-wavelength anomalous diffraction (native-SAD) phasing of serial femtosecond crystallography (SFX) data. In this work, sensitive anomalous data-quality indicators and model proteins were used to quantify improvements in native-SAD at XFELs such as utilization of longer wavelengths, careful experimental geometry optimization, and better post-refinement and partiality correction. Compared with studies using shorter wavelengths at other XFELs and older software versions, up to one order of magnitude reduction in the required number of indexed images for native-SAD was achieved, hence lowering sample consumption and beam-time requirements significantly. Improved data quality and higher anomalous signal facilitate so-far underutilized de novo structure determination of challenging proteins at XFELs. Improvements presented in this work can be used in other types of SFX experiments that require accurate measurements of weak signals, for example time-resolved studies.

---

Organizational Affiliation: 

Photon Science Division, Paul Scherrer Institut, Forschungsstrasse 111, Villigen PSI, 5232, Switzerland.

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: 2.65 Å
• R-Value Free: 0.196 
• R-Value Work: 0.153 
• R-Value Observed: 0.155 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.5	α = 90
b = 58.5	β = 90
c = 151.25	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling
CRANK2	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2019-06-18 
• Released Date: 2020-07-15 
Deposition Author(s): Nass, K., Cheng, R., Vera, L., Mozzanica, A., Redford, S., Ozerov, D., Basu, S., James, D., Knopp, G., Cirelli, C., Martiel, I., Casadei, C., Weinert, T., Nogly, P., Skopintsev, P., Usov, I., Leonarski, F., Geng, T., Rappas, M., Dore, A.S., Cooke, R., Nasrollahi Shirazi, S., Dworkowski, F., Sharpe, M., Olieric, N., Steinmetz, M.O., Schertler, G., Abela, R., Patthey, L., Schmitt, B., Hennig, M., Standfuss, J., Wang, M., Milne, J.C.

Revision History  

• Version 1.0: 2020-07-15
  Type: Initial release
  
• Version 1.1: 2020-12-02
  Changes: Database references