4ZXR | pdb_00004zxr

Structure of Thaumatin wrapped in graphene within vacuum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 
    0.175 (Depositor), 0.163 (DCC) 
  • R-Value Work: 
    0.146 (Depositor), 0.158 (DCC) 
  • R-Value Observed: 
    0.148 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 4ZXR

This is version 1.3 of the entry. See complete history

Literature

In vacuo X-ray data collection from graphene-wrapped protein crystals.

Warren, A.J.Crawshaw, A.D.Trincao, J.Aller, P.Alcock, S.Nistea, I.Salgado, P.S.Evans, G.

(2015) Acta Crystallogr D Biol Crystallogr 71: 2079-2088

  • DOI: https://doi.org/10.1107/S1399004715014194
  • Primary Citation Related Structures: 
    4ZXR

  • PubMed Abstract: 

    The measurement of diffraction data from macromolecular crystal samples held in vacuo holds the promise of a very low X-ray background and zero absorption of incident and scattered beams, leading to better data and the potential for accessing very long X-ray wavelengths (>3 Å) for native sulfur phasing. Maintaining the hydration of protein crystals under vacuum is achieved by the use of liquid jets, as with serial data collection at free-electron lasers, or is side-stepped by cryocooling the samples, as implemented at new synchrotron beamlines. Graphene has been shown to protect crystals from dehydration by creating an extremely thin layer that is impermeable to any exchanges with the environment. Furthermore, owing to its hydrophobicity, most of the aqueous solution surrounding the crystal is excluded during sample preparation, thus eliminating most of the background caused by liquid. Here, it is shown that high-quality data can be recorded at room temperature from graphene-wrapped protein crystals in a rough vacuum. Furthermore, it was observed that graphene protects crystals exposed to different relative humidities and a chemically harsh environment.


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

Macromolecule Content 

  • Total Structure Weight: 22.56 kDa 
  • Atom Count: 1,635 
  • 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
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free:  0.175 (Depositor), 0.163 (DCC) 
  • R-Value Work:  0.146 (Depositor), 0.158 (DCC) 
  • R-Value Observed: 0.148 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.079α = 90
b = 59.079β = 90
c = 151.22γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-14
    Type: Initial release
  • Version 1.1: 2015-10-28
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-11-13
    Changes: Structure summary