3WPL

SPATIOTEMPORAL DEVELOPMENT of SOAKED PROTEIN CRYSTAL; 2510 SEC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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, 3WU7, 3WU8, 3WU9, 3WUA

  • 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 ...

    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

    Department of Applied Biochemistry, School of Engineering, Tokai University, Kitakaname 4-1-1, Hiratsuka, Kanagawa 259-1292, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme C
A
129Gallus gallusGene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Go to Gene View: LYZ
Go to UniProtKB:  P00698
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PT4
Query on PT4

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.173 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 79.303α = 90.00
b = 79.303β = 90.00
c = 37.805γ = 90.00
Software Package:
Software NamePurpose
BSSdata collection
SCALEPACKdata scaling
HKL-2000data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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