Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 11.57 kDa 
• Atom Count: 899 
• Modelled Residue Count: 105 
• Deposited Residue Count: 105 
• Unique protein chains: 1

3L45

A Joint Neutron and X-ray structure of Oxidized Amicyanin

• PDB DOI: 10.2210/pdb3L45/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Paracoccus denitrificans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-12-18 Released: 2010-04-28 
• Deposition Author(s): Sukumar, N., Mathews, F.S., Langan, P., Davidson, V.L.

---

Experimental Data Snapshot

• Method: NEUTRON DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.234 
• R-Value Work: 0.209 
• R-Value Observed: 0.209 

---

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.215 
• R-Value Work: 0.198 

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 U S A 107: 6817-6822

• PubMed: 20351252 
• DOI: 10.1073/pnas.0912672107
• Primary Citation of Related Structures:  
  3L45


• 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 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 D Biol Crystallogr 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. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amicyanin	A	105	Paracoccus denitrificans	Mutation(s): 0  Gene Names: ami, mauC
UniProt
Find proteins for P22364 (Paracoccus denitrificans) Explore P22364  Go to UniProtKB:  P22364

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CU	B [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: NEUTRON DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.234 
• R-Value Work: 0.209 
• R-Value Observed: 0.209 
• Space Group: P 1 2₁ 1

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.215 
• R-Value Work: 0.198 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.54	α = 90
b = 56.58	β = 96.21
c = 28.86	γ = 90

Software Package:

Software Name	Purpose
nCNS	refinement
HKL-2000	data reduction
d*TREK	data reduction
HKL-2000	data scaling
LAUENORM	data scaling
SCALA	data scaling
EPMR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-12-18 
• Released Date: 2010-04-28 
Deposition Author(s): Sukumar, N., Mathews, F.S., Langan, P., Davidson, V.L.

Revision History  

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