Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 23276.22 
• Atom Count: 1517 
• Residue Count: 200 
• Unique protein chains: 1

2Q4S

Ensemble refinement of the protein crystal structure of cysteine dioxygenase type I from Mus musculus Mm.241056

• DOI: 10.2210/pdb2Q4S/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli


• Deposited: 2007-05-31 Released: 2007-06-19 
• Deposition Author(s): Levin, E.J., Kondrashov, D.A., Wesenberg, G.E., Phillips Jr., G.N., Center for Eukaryotic Structural Genomics (CESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.211 
• R-Value Work: 0.159 

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

• 2ATF - determined by Wesenberg, G.E., Phillips Jr., G.N., Mccoy, J.G., Bitto, E., Bingman, C.A., Allard, S.T.M., Center for Eukaryotic Structural Genomics (CESG)  

Literature

Ensemble refinement of protein crystal structures: validation and application.

Levin, E.J., Kondrashov, D.A., Wesenberg, G.E., Phillips, G.N.

(2007) Structure 15: 1040-1052

• PubMed: 17850744 
• DOI: 10.1016/j.str.2007.06.019
• Primary Citation of Related Structures:  
  2Q52, 2Q51, 2Q50, 2Q4Z, 2Q4Y, 2Q4X, 2Q4V, 2Q4U, 2Q4T, 2Q4R, 2Q4Q, 2Q4P, 2Q4O, 2Q4N, 2Q4M, 2Q4L, 2Q4K, 2Q4J, 2Q4I, 2Q4H, 2Q4F, 2Q4E, 2Q4D, 2Q4C, 2Q4B, 2Q49, 2Q4A, 2Q48, 2Q47, 2Q46, 2Q45, 2Q44, 2Q43, 2Q42, 2Q41, 2Q40, 2Q3W, 2Q3V, 2Q3U, 2Q3T,
  2Q52, 2Q51, 2Q50, 2Q4Z, 2Q4Y, 2Q4X, 2Q4V, 2Q4U, 2Q4T, 2Q4R, 2Q4Q, 2Q4P, 2Q4O, 2Q4N, 2Q4M, 2Q4L, 2Q4K, 2Q4J, 2Q4I, 2Q4H, 2Q4F, 2Q4E, 2Q4D, 2Q4C, 2Q4B, 2Q49, 2Q4A, 2Q48, 2Q47, 2Q46, 2Q45, 2Q44, 2Q43, 2Q42, 2Q41, 2Q40, 2Q3W, 2Q3V, 2Q3U, 2Q3T, 2Q3S, 2Q3R, 2Q3Q, 2Q3P, 2Q3O, 2Q3M
• Also Cited By: 2Q53, 2Q4W, 2Q4G


• PubMed Abstract: 
  

X-ray crystallography typically uses a single set of coordinates and B factors to describe macromolecular conformations. Refinement of multiple copies of the entire structure has been previously used in specific cases as an alternative means of representing structural flexibility. Here, we systematically validate this method by using simulated diffraction data, and we find that ensemble refinement produces better representations of the distributions of atomic positions in the simulated structures than single-conformer refinements. Comparison of principal components calculated from the refined ensembles and simulations shows that concerted motions are captured locally, but that correlations dissipate over long distances. Ensemble refinement is also used on 50 experimental structures of varying resolution and leads to decreases in R(free) values, implying that improvements in the representation of flexibility observed for the simulated structures may apply to real structures. These gains are essentially independent of resolution or data-to-parameter ratio, suggesting that even structures at moderate resolution can benefit from ensemble refinement.

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Related Citations: 

• Structure and mechanism of mouse cysteine dioxygenase.
  McCoy, J.G.,Bailey, L.J.,Bitto, E.,Bingman, C.A.,Aceti, D.J.,Fox, B.G.,Phillips, G.N.
  (2006) Proc.Natl.Acad.Sci.Usa 103: 3084




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Organizational Affiliation: 

Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Cysteine dioxygenase type 1	A	200	Mus musculus	Mutation(s): 0  Gene Names: Cdo1 EC: 1.13.11.20
Find proteins for P60334 (Mus musculus) Go to UniProtKB:  P60334

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
EDO	A	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NI	A	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.211 
• R-Value Work: 0.159 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 57.550	α = 90.00
b = 57.550	β = 90.00
c = 122.076	γ = 90.00

Software Package:

Software Name	Purpose
CNS	refinement
CNS	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-05-31 
• Released Date: 2007-06-19 
• Deposition Author(s): Levin, E.J., Kondrashov, D.A., Wesenberg, G.E., Phillips Jr., G.N., Center for Eukaryotic Structural Genomics (CESG)

Revision History 

• Version 1.0: 2007-06-19
  Type: Initial release
• Version 1.1: 2007-09-25
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2011-08-10
  Type: Other