5N0K

Rat ceruloplasmin orthorhombic form

• PDB DOI: https://doi.org/10.2210/pdb5N0K/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Rattus norvegicus
• Mutation(s): No 


• Deposited: 2017-02-03 Released: 2017-12-13 
• Deposition Author(s): Samygina, V.R., Sokolov, A.V., Bourenkov, G., Vasilyev, V.B.
• Funding Organization(s): RFBR

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.226 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 

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

• PubMed: 29177316 
• DOI: https://doi.org/10.1039/c7mt00157f
• Primary Citation of Related Structures:  
  5N0K, 5N4L


• 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), 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.

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Organizational Affiliation: 

Shubnikov Institute of Crystallography of FSRC "Crystallography and Photonics" RAS, Leninsky pr.59, Moscow 117333, Russia. [e-mail] and NRC Kurchatov Institute, Kurchatov pl. 1, Moscow 123098, Russia.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 121.69 kDa 
• Atom Count: 8,566 
• Modelled Residue Count: 1,034 
• Deposited Residue Count: 1,059 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ceruloplasmin	A	1,059	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for P13635 (Rattus norvegicus) Explore P13635  Go to UniProtKB:  P13635

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CU	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
CA	L [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	M [auth A], N [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.226 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.36	α = 90
b = 103.81	β = 90
c = 172.811	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-12-13 
Deposition Author(s): Samygina, V.R., Sokolov, A.V., Bourenkov, G., Vasilyev, V.B.

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Funding Organization	Location	Grant Number
RFBR	Russian Federation	15-54-74006

Revision History  

• Version 1.0: 2017-12-13
  Type: Initial release
  
• Version 1.1: 2017-12-27
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2024-01-17
  Changes: Data collection, Database references, Refinement description, Structure summary