4R6C

X-ray diffraction in temporally and spatially resolved biomolecular science: the X-ray crystal structure of hen egg white lysozyme cocrystallized with Ta6Br12 and then a crystal soaked in K2PtBr6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

X-ray diffraction in temporally and spatially resolved biomolecular science.

Helliwell, J.R.Brink, A.Kaenket, S.Starkey, V.L.Tanley, S.W.

(2015) Faraday Discuss 177: 429-441

  • DOI: 10.1039/c4fd00166d

  • PubMed Abstract: 
  • Time-resolved Laue protein crystallography at the European Synchrotron Radiation Facility (ESRF) opened up the field of sub-nanosecond protein crystal structure analyses. There are a limited number of such time-resolved studies in the literature. Why ...

    Time-resolved Laue protein crystallography at the European Synchrotron Radiation Facility (ESRF) opened up the field of sub-nanosecond protein crystal structure analyses. There are a limited number of such time-resolved studies in the literature. Why is this? The X-ray laser now gives us femtosecond (fs) duration pulses, typically 10 fs up to ∼50 fs. Their use is attractive for the fastest time-resolved protein crystallography studies. It has been proposed that single molecules could even be studied with the advantage of being able to measure X-ray diffraction from a 'crystal lattice free' single molecule, with or without temporal resolved structural changes. This is altogether very challenging R&D. So as to assist this effort we have undertaken studies of metal clusters that bind to proteins, both 'fresh' and after repeated X-ray irradiation to assess their X-ray-photo-dynamics, namely Ta6Br12, K2PtI6 and K2PtBr6 bound to a test protein, hen egg white lysozyme. These metal complexes have the major advantage of being very recognisable shapes (pseudo spherical or octahedral) and thereby offer a start to (probably very difficult) single molecule electron density map interpretations, both static and dynamic. A further approach is to investigate the X-ray laser beam diffraction strength of a well scattering nano-cluster; an example from nature being the iron containing ferritin. Electron crystallography and single particle electron microscopy imaging offers alternatives to X-ray structural studies; our structural studies of crustacyanin, a 320 kDa protein carotenoid complex, can be extended either by electron based techniques or with the X-ray laser representing a fascinating range of options. General outlook remarks concerning X-ray, electron and neutron macromolecular crystallography as well as 'NMR crystallography' conclude the article.


    Organizational Affiliation

    School of Chemistry, University of Manchester M13 9PL, UK. john.helliwell@manchester.ac.uk.




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 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TBR
Query on TBR

Download SDF File 
Download CCD File 
A
HEXATANTALUM DODECABROMIDE
DODECABROMOHEXATANTALUM
Br12 Ta6
YWYIQTPPCOBSGN-UHFFFAOYSA-M
 Ligand Interaction
6BP
Query on 6BP

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Download CCD File 
A
HEXABROMOPLATINATE(IV)
Br6 Pt
VOEHEFXBCNCSCK-UHFFFAOYSA-H
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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

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Download CCD File 
A
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.180 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 79.070α = 90.00
b = 79.070β = 90.00
c = 37.235γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
SAINTdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-08-24 
  • Released Date: 2015-02-04 
  • Deposition Author(s): Helliwell, J.R.

Revision History 

  • Version 1.0: 2015-02-04
    Type: Initial release
  • Version 1.1: 2015-04-29
    Type: Database references