5N4L | pdb_00005n4l

Rat ceruloplasmin trigonal form

• PDB DOI: https://doi.org/10.2210/pdb5N4L/pdb

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


• Deposited: 2017-02-11 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: 3.20 Å
• R-Value Free: 
  0.265 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.193 (Depositor) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

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 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.
Institute of Experimental Medicine, ul. Academica Pavlova, 12, Saint-Petersburg 197376, Russia and Saint-Petersburg State Universisty, Universitetskaya nab. 7-9, Saint-Petersburg 199034, Russia and Centre of Preclinical Translational Research, Almazov National Medical Research Centre, ul. Dolgoozernaya, 43, Saint-Petersburg 197371, Russia.
EMBL, Notkestrasse 85, 22607 Hamburg, Germany.
Shubnikov Institute of Crystallography of FSRC "Crystallography and Photonics" RAS, Leninsky pr.59, Moscow 117333, Russia. [e-mail] and Belozersky Institute of Physico-Chemical Biology and Department of Chemistry, Lomonosov Moscow State University, Moscow 119899, Russia.
Institute of Experimental Medicine, ul. Academica Pavlova, 12, Saint-Petersburg 197376, Russia.
Institute of Experimental Medicine, ul. Academica Pavlova, 12, Saint-Petersburg 197376, Russia and Saint-Petersburg State Universisty, Universitetskaya nab. 7-9, Saint-Petersburg 199034, Russia.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 236.83 kDa 
• Atom Count: 16,660 
• Modeled Residue Count: 2,068 
• Deposited Residue Count: 2,068 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ceruloplasmin	A, B	1,034	Rattus norvegicus	Mutation(s): 0  EC: 1.16.3.1 (UniProt), 1.16.3.4 (UniProt), 1.11.1.27 (UniProt), 1.11.1.9 (UniProt)
UniProt
Find proteins for P13635 (Rattus norvegicus) Explore P13635  Go to UniProtKB:  P13635

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CU	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
CA	H [auth A], P [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	I [auth A], Q [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.265 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.193 (Depositor) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.23	α = 90
b = 128.23	β = 90
c = 407.66	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
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: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary