5N0K

Rat ceruloplasmin orthorhombic form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Rat ceruloplasmin: a new labile copper binding site and zinc/copper mosaic.

Samygina, V.R.Sokolov, A.V.Bourenkov, G.Schneider, T.R.Anashkin, V.A.Kozlov, S.O.Kolmakov, N.N.Vasilyev, V.B.

(2017) Metallomics 9: 1828-1838

  • DOI: 10.1039/c7mt00157f
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ceruloplasmin (Cp) is a copper-containing multifunctional oxidase of plasma, an antioxidant, an acute-phase protein and a free radical scavenger. The structural organization of Cp causes its sensitivity to proteolysis and ROS (reactive oxygen species ...

    Ceruloplasmin (Cp) is a copper-containing multifunctional oxidase of plasma, an antioxidant, an acute-phase protein and a free radical scavenger. The structural organization of Cp causes its sensitivity to proteolysis and ROS (reactive oxygen species), which can alter some of the important Cp functions. Elucidation of the orthorhombic crystal structure of rat Cp at 2.3 Å resolution revealed the basis for stronger resistance of rat Cp to proteolysis and a new labile copper binding site. The presence of this site appears as a very rare and distinctive feature of rat Cp as was shown by sequence alignment of ceruloplasmin, hephaestin and zyklopen in the Deuterostomia taxonomic group. The trigonal crystal form of rat Cp at 3.2 Å demonstrates unexpected partial substitution of copper by zinc.


    Organizational Affiliation

    Shubnikov Institute of Crystallography of FSRC "Crystallography and Photonics" RAS, Leninsky pr.59, Moscow 117333, Russia. lera@ns.crys.ras.ru and NRC Kurchatov Institute, Kurchatov pl. 1, Moscow 123098, Russia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ceruloplasmin
A
1059Rattus norvegicusMutation(s): 0 
Gene Names: Cp
EC: 1.16.3.1
Find proteins for P13635 (Rattus norvegicus)
Go to UniProtKB:  P13635
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

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Download CCD File 
A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 75.360α = 90.00
b = 103.810β = 90.00
c = 172.811γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
RFBRRussian Federation15-54-74006

Revision History 

  • Version 1.0: 2017-12-13
    Type: Initial release
  • Version 1.1: 2017-12-27
    Type: Database references