4XFA | pdb_00004xfa

cysteine dioxygenase variant - Y157F at pH 8.0 in complex with homocysteine

• PDB DOI: https://doi.org/10.2210/pdb4XFA/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-12-26 Released: 2016-02-24 
• Deposition Author(s): Driggers, C.M., Karplus, P.A.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.210 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Structures of Mammalian Cysteine Dioxygenase Variants Missing the Cys-Tyr Crosslink

Driggers, C.M., Hischberger, L.L., Stipanuk, M.H., Karplus, P.A.

To be published.

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: 23.23 kDa 
• Atom Count: 1,749 
• Modeled Residue Count: 186 
• Deposited Residue Count: 200 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteine dioxygenase type 1	A	200	Rattus norvegicus	Mutation(s): 1  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
HCS	C [auth A]	2-AMINO-4-MERCAPTO-BUTYRIC ACID C4 H9 N O2 S FFFHZYDWPBMWHY-VKHMYHEASA-N
FE	B [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.210 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.6	α = 90
b = 57.6	β = 90
c = 122.4	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-02-24 
Deposition Author(s): Driggers, C.M., Karplus, P.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	NIH-DK-056649
Department of Energy (DOE, United States)	United States	DE-AC02-98CH10886

Revision History  

• Version 1.0: 2016-02-24
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2019-12-04
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2023-11-15
  Changes: Data collection
• Version 1.5: 2024-04-03
  Changes: Structure summary