Thaumatin structure determined by SACLA at 1.55 Angstrom

Experimental Data Snapshot

  • Resolution: 1.55 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.127 
  • R-Value Observed: 0.128 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Hydroxyethyl cellulose matrix applied to serial crystallography

Sugahara, M.Nakane, T.Masuda, T.Suzuki, M.Inoue, S.Song, C.Tanaka, R.Nakatsu, T.Mizohata, E.Yumoto, F.Tono, K.Joti, Y.Kameshima, T.Hatsui, T.Yabashi, M.Nureki, O.Numata, K.Nango, E.Iwata, S.

(2017) Sci Rep 7: 703-703

  • DOI: https://doi.org/10.1038/s41598-017-00761-0
  • Primary Citation of Related Structures:  
    5WR8, 5WR9, 5WRA, 5WRB, 5WRC

  • PubMed Abstract: 

    Serial femtosecond crystallography (SFX) allows structures of proteins to be determined at room temperature with minimal radiation damage. A highly viscous matrix acts as a crystal carrier for serial sample loading at a low flow rate that enables the determination of the structure, while requiring consumption of less than 1 mg of the sample. However, a reliable and versatile carrier matrix for a wide variety of protein samples is still elusive. Here we introduce a hydroxyethyl cellulose-matrix carrier, to determine the structure of three proteins. The de novo structure determination of proteinase K from single-wavelength anomalous diffraction (SAD) by utilizing the anomalous signal of the praseodymium atom was demonstrated using 3,000 diffraction images.

  • Organizational Affiliation

    Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thaumatin I207Thaumatococcus danielliiMutation(s): 0 
Find proteins for P02883 (Thaumatococcus daniellii)
Explore P02883 
Go to UniProtKB:  P02883
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02883
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on TLA

Download Ideal Coordinates CCD File 
C4 H6 O6
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.459α = 90
b = 58.459β = 90
c = 151.639γ = 90
Software Package:
Software NamePurpose
CrystFELdata reduction
CrystFELdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-29
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Data collection
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references