3WUA

Spatiotemporal development of soaked protein crystal; derivative 3610 sec


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

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Literature

Spatiotemporal development of soaked protein crystal

Mizutani, R.Shimizu, Y.Saiga, R.Ueno, G.Nakamura, Y.Takeuchi, A.Uesugi, K.Suzuki, Y.

(2014) Sci Rep 4: 5731-5731

  • DOI: 10.1038/srep05731
  • Primary Citation of Related Structures:  
    3WPJ, 3WPK, 3WPL, 3WUA, 3WU9, 3WU7, 3WU8

  • PubMed Abstract: 
  • Crystal soaking is widely performed in biological crystallography. This paper reports time-resolved X-ray crystallographic and microtomographic analyses of tetragonal crystals of chicken egg-white lysozyme soaked in mother liquor containing potassium hex ...

    Crystal soaking is widely performed in biological crystallography. This paper reports time-resolved X-ray crystallographic and microtomographic analyses of tetragonal crystals of chicken egg-white lysozyme soaked in mother liquor containing potassium hexachloroplatinate. The microtomographic analysis showed that X-ray attenuation spread from the superficial layer of the crystal and then to the crystal core. The crystallographic analyses indicated that platinum sites can be classified into two groups from the temporal development of the electron densities. A soaking process consisting of binding-rate-driven and equilibrium-driven layers is proposed to describe these results. This study suggests that the composition of chemical and structural species resulting from the soaking process varies depending on the position in the crystal.


    Organizational Affiliation

    Research and Utilization Division, JASRI/SPring-8, Kouto 1-1-1, Sayo, Hyogo 679-5198, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lysozyme C A129Gallus gallusMutation(s): 0 
Gene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PT4
Query on PT4

Download Ideal Coordinates CCD File 
A
PLATINUM (IV) ION
Pt
NDBYXKQCPYUOMI-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.334α = 90
b = 79.334β = 90
c = 37.763γ = 90
Software Package:
Software NamePurpose
BSSdata collection
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-30
    Type: Initial release