5AI3

X-ray structure of 113Cd-substituted Perdeuterated Pyrococcus furiosus rubredoxin to 1.02A resolution at 295K in a quartz capillary


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.02 Å
  • R-Value Free: 0.126 
  • R-Value Work: 0.106 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Macromolecular Structure Phasing by Neutron Anomalous Diffraction.

Cuypers, M.G.Mason, S.A.Mossou, E.Haertlein, M.Forsyth, V.T.Mitchell, E.P.

(2016) Sci.Rep. 6: 31487

  • DOI: 10.1038/srep31487
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In this report we show for the first time that neutron anomalous dispersion can be used in a practical manner to determine experimental phases of a protein crystal structure, providing a new tool for structural biologists. The approach is demonstrate ...

    In this report we show for the first time that neutron anomalous dispersion can be used in a practical manner to determine experimental phases of a protein crystal structure, providing a new tool for structural biologists. The approach is demonstrated through the use of a state-of-the-art monochromatic neutron diffractometer at the Institut Laue-Langevin (ILL) in combination with crystals of perdeuterated protein that minimise the level of hydrogen incoherent scattering and enhance the visibility of the anomalous signal. The protein used was rubredoxin in which cadmium replaced the iron at the iron-sulphur site. While this study was carried out using a steady-state neutron beam source, the results will be of major interest for capabilities at existing and emerging spallation neutron sources where time-of-flight instruments provide inherent energy discrimination. In particular this capability may be expected to offer unique opportunities to a rapidly developing structural biology community where there is increasing interest in the identification of protonation states, protein/water interactions and protein-ligand interactions - all of which are of central importance to a wide range of fundamental and applied areas in the biosciences.


    Organizational Affiliation

    Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RUBREDOXIN
A
54Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Gene Names: rub
Find proteins for P24297 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  P24297
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CD
Query on CD

Download SDF File 
Download CCD File 
A
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.02 Å
  • R-Value Free: 0.126 
  • R-Value Work: 0.106 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 34.443α = 90.00
b = 35.141β = 90.00
c = 43.785γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-02
    Type: Initial release
  • Version 1.1: 2016-03-16
    Type: Atomic model
  • Version 1.2: 2016-08-24
    Type: Database references