4YNI

Iron free succinate bound rat cysteine dioxygenase

• PDB DOI: https://doi.org/10.2210/pdb4YNI/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-03-10 Released: 2016-03-23 
• Deposition Author(s): Fellner, M., Tchesnokov, E.P., Jameson, G.N.L., Wilbanks, S.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.224 
• R-Value Work: 0.175 
• R-Value Observed: 0.178 

Starting Model: experimental

Literature

Iron free succinate bound rat cysteine dioxygenase

Fellner, M., Tchesnokov, E.P., Jameson, G.N.L., Wilbanks, S.M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 24.4 kDa 
• Atom Count: 1,646 
• Modelled Residue Count: 187 
• Deposited Residue Count: 210 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteine dioxygenase type 1	A	210	Rattus norvegicus	Mutation(s): 0  Gene Names: Cdo1 EC: 1.13.11.20
UniProt
Find proteins for P21816 (Rattus norvegicus) Explore P21816  Go to UniProtKB:  P21816

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SIN	C [auth A]	SUCCINIC ACID C4 H6 O4 KDYFGRWQOYBRFD-UHFFFAOYSA-N
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.224 
• R-Value Work: 0.175 
• R-Value Observed: 0.178 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.69	α = 90
b = 57.69	β = 90
c = 121.87	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-23 
Deposition Author(s): Fellner, M., Tchesnokov, E.P., Jameson, G.N.L., Wilbanks, S.M.

Revision History  

• Version 1.0: 2016-03-23
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary