5TCL | pdb_00005tcl

Thaumatin from 4.96 A wavelength data collection


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.246 (Depositor), 0.258 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Long-wavelength macromolecular crystallography - First successful native SAD experiment close to the sulfur edge.

Aurelius, O.Duman, R.El Omari, K.Mykhaylyk, V.Wagner, A.

(2017) Nucl Instrum Methods Phys Res B 411: 12-16

  • DOI: https://doi.org/10.1016/j.nimb.2016.12.005
  • Primary Citation Related Structures: 
    5TCL

  • PubMed Abstract: 

    Phasing of novel macromolecular crystal structures has been challenging since the start of structural biology. Making use of anomalous diffraction of natively present elements, such as sulfur and phosphorus, for phasing has been possible for some systems, but hindered by the necessity to access longer X-ray wavelengths in order to make most use of the anomalous scattering contributions of these elements. Presented here are the results from a first successful experimental phasing study of a macromolecular crystal structure at a wavelength close to the sulfur K edge. This has been made possible by the in-vacuum setup and the long-wavelength optimised experimental setup at the I23 beamline at Diamond Light Source. In these early commissioning experiments only standard data collection and processing procedures have been applied, in particular no dedicated absorption correction has been used. Nevertheless the success of the experiment demonstrates that the capability to extract phase information can be even further improved once data collection protocols and data processing have been optimised.


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

Macromolecule Content 

  • Total Structure Weight: 22.47 kDa 
  • Atom Count: 1,575 
  • Modeled Residue Count: 207 
  • Deposited Residue Count: 207 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Thaumatin-1207Thaumatococcus danielliiMutation(s): 0 
UniProt
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
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.246 (Depositor), 0.258 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.769α = 90
b = 57.769β = 90
c = 150.512γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
SHARPphasing
Cootmodel building
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-20
    Type: Initial release
  • Version 1.1: 2018-01-03
    Changes: Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-11-13
    Changes: Structure summary