4EKT

Final Thaumatin Structure for Radiation Damage Experiment at 180 K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Spatial distribution of radiation damage to crystalline proteins at 25-300 K.

Warkentin, M.Badeau, R.Hopkins, J.B.Thorne, R.E.

(2012) Acta Crystallogr D Biol Crystallogr 68: 1108-1117

  • DOI: 10.1107/S0907444912021361
  • Primary Citation of Related Structures:  
    4EP8, 4EPB, 4EPD, 4EPE, 4EK0, 4EL3, 4EKT, 4EL7, 4EKO, 4EL2

  • PubMed Abstract: 
  • The spatial distribution of radiation damage (assayed by increases in atomic B factors) to thaumatin and urease crystals at temperatures ranging from 25 to 300 K is reported. The nature of the damage changes dramatically at approximately 180 K. Above this temperature the role of solvent diffusion is apparent in thaumatin crystals, as solvent-exposed turns and loops are especially sensitive ...

    The spatial distribution of radiation damage (assayed by increases in atomic B factors) to thaumatin and urease crystals at temperatures ranging from 25 to 300 K is reported. The nature of the damage changes dramatically at approximately 180 K. Above this temperature the role of solvent diffusion is apparent in thaumatin crystals, as solvent-exposed turns and loops are especially sensitive. In urease, a flap covering the active site is the most sensitive part of the molecule and nearby loops show enhanced sensitivity. Below 180 K sensitivity is correlated with poor local packing, especially in thaumatin. At all temperatures, the component of the damage that is spatially uniform within the unit cell accounts for more than half of the total increase in the atomic B factors and correlates with changes in mosaicity. This component may arise from lattice-level, rather than local, disorder. The effects of primary structure on radiation sensitivity are small compared with those of tertiary structure, local packing, solvent accessibility and crystal contacts.


    Organizational Affiliation

    Physics Department, Cornell University, Ithaca, NY 14853, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thaumatin-1A207Thaumatococcus danielliiMutation(s): 0 
Find proteins for P02883 (Thaumatococcus daniellii)
Explore P02883 
Go to UniProtKB:  P02883
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TLA
Query on TLA

Download Ideal Coordinates CCD File 
B [auth A]L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.9α = 90
b = 57.9β = 90
c = 150.07γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
DENZOdata reduction
BUSTERphasing
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-29
    Type: Initial release
  • Version 1.1: 2013-01-23
    Changes: Database references