4DT3

Crystal structure of zinc-charged lysozyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Experimental phasing using zinc anomalous scattering

Cha, S.S.An, Y.J.Jeong, C.S.Kim, M.K.Lee, S.G.Lee, K.H.Oh, B.H.

(2012) Acta Crystallogr.,Sect.D 68: 1253-1258

  • DOI: 10.1107/S0907444912024420
  • Primary Citation of Related Structures:  
  • Also Cited By: 5GL4, 5GL3, 5GL2, 5GKX

  • PubMed Abstract: 
  • Zinc is a suitable metal for anomalous dispersion phasing methods in protein crystallography. Structure determination using zinc anomalous scattering has been almost exclusively limited to proteins with intrinsically bound zinc(s). Here, it is report ...

    Zinc is a suitable metal for anomalous dispersion phasing methods in protein crystallography. Structure determination using zinc anomalous scattering has been almost exclusively limited to proteins with intrinsically bound zinc(s). Here, it is reported that multiple zinc ions can easily be charged onto the surface of proteins with no intrinsic zinc-binding site by using zinc-containing solutions. Zn derivatization of protein surfaces appears to be a largely unnoticed but promising method of protein structure determination.


    Organizational Affiliation

    Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Ansan 426-744, Republic of Korea. chajung@kordi.re.kr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme C
A
129Gallus gallusMutation(s): 0 
Gene 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.183 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 79.102α = 90.00
b = 79.102β = 90.00
c = 36.816γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
SHELXSphasing
HKL-2000data reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-09-12
    Type: Initial release
  • Version 1.1: 2013-07-24
    Type: Database references