3L45

A Joint Neutron and X-ray structure of Oxidized Amicyanin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.198 
  • Method: NEUTRON DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

A joint x-ray and neutron study on amicyanin reveals the role of protein dynamics in electron transfer.

Sukumar, N., Mathews, F.S., Langan, P., Davidson, V.L.

(2010) Proc.Natl.Acad.Sci.USA 107: 6817-6822

  • DOI: 10.1073/pnas.0912672107

  • PubMed Abstract: 

    • The joint x-ray/neutron diffraction model of the Type I copper protein, amicyanin from Paracoccus denitrificans was determined at 1.8 A resolution. The protein was crystallized using reagents prepared in D(2)O. About 86% of the amide hydrogen atoms a ...

    The joint x-ray/neutron diffraction model of the Type I copper protein, amicyanin from Paracoccus denitrificans was determined at 1.8 A resolution. The protein was crystallized using reagents prepared in D(2)O. About 86% of the amide hydrogen atoms are either partially or fully exchanged, which correlates well with the atomic depth of the amide nitrogen atom and the secondary structure type, but with notable exceptions. Each of the four residues that provide copper ligands is partially deuterated. The model reveals the dynamic nature of the protein, especially around the copper-binding site. A detailed analysis of the presence of deuterated water molecules near the exchange sites indicates that amide hydrogen exchange is primarily due to the flexibility of the protein. Analysis of the electron transfer path through the protein shows that residues in that region are highly dynamic, as judged by hydrogen/deuterium exchange. This could increase the rate of electron transfer by transiently shortening through-space jumps in pathways or by increasing the atomic packing density. Analysis of C-HX bonding reveals previously undefined roles of these relatively weak H bonds, which, when present in sufficient number can collectively influence the structure, redox, and electron transfer properties of amicyanin.

    Related Citations: 
    • A preliminary time-of-flight neutron diffraction study on amicyanin from Paracoccus denitrificans
      Sukumar, N.,Langan, P.,Mathews, F.S.,Jones, L.H.,Thiyagarajan, P.,Schoenborn, B.P.,Davidson, V.L.
      (2005) Acta Crystallogr.,Sect.D 61: 640

    Organizational Affiliation: 

    Northeastern Collaborative Access Team and Department of Chemistry and Chemical Biology, Cornell University, Building 436E, Argonne National Laboratory, Argonne, IL 60439, USA. sukumar@anl.gov




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Amicyanin
A
105Paracoccus denitrificansMutation(s): 0 
Gene Names: mauC (ami)
Find proteins for P22364 (Paracoccus denitrificans)
Go to UniProtKB:  P22364
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CU
Query on CU
Download SDF File 
Download CCD File 
A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
DOD
Query on DOD
Download SDF File 
Download CCD File 
A
DEUTERATED WATER
D2 O
XLYOFNOQVPJJNP-ZSJDYOACSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 27.540α = 90.00
b = 56.580β = 96.21
c = 28.860γ = 90.00
  • Method: NEUTRON DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.209 
Software Package:
Software NamePurpose
SCALAdata scaling
HKL-2000data reduction
EPMRphasing
d*TREKdata reduction
LAUENORMdata scaling
nCNSrefinement
HKL-2000data scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Data collection, Version format compliance
  • Version 1.2: 2018-04-25
    Type: Data collection