3EQE

Crystal structure of the YubC protein from Bacillus subtilis. Northeast Structural Genomics Consortium target SR112.

• PDB DOI: https://doi.org/10.2210/pdb3EQE/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-09-30 Released: 2008-10-14 
• Deposition Author(s): Vorobiev, S.M., Su, M., Seetharaman, J., Benach, J., Forouhar, F., Clayton, G., Cooper, B., Wang, H., Foote, E.L., Ciccosanti, C., Mao, L., Xiao, R., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.82 Å
• R-Value Free: 0.296 
• R-Value Work: 0.241 
• R-Value Observed: 0.241 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 4QM8

Literature

Crystal structure of the YubC protein from Bacillus subtilis.

Vorobiev, S.M., Su, M., Seetharaman, J., Benach, J., Forouhar, F., Clayton, G., Cooper, B., Wang, H., Foote, E.L., Ciccosanti, C., Mao, L., Xiao, R., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L.

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)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 39.45 kDa 
• Atom Count: 2,446 
• Modelled Residue Count: 310 
• Deposited Residue Count: 342 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative cystein dioxygenase	A, B	171	Bacillus subtilis	Mutation(s): 0  Gene Names: BSU31140, yubC EC: 1.13.11 (PDB Primary Data), 1.13.11.20 (UniProt)
UniProt
Find proteins for O32085 (Bacillus subtilis (strain 168)) Explore O32085  Go to UniProtKB:  O32085

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE	C [auth A], D [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.82 Å
• R-Value Free: 0.296 
• R-Value Work: 0.241 
• R-Value Observed: 0.241 
• Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.83	α = 90
b = 65.83	β = 90
c = 197.19	γ = 90

Software Package:

Software Name	Purpose
SHELXDE	phasing
CNS	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-14 
Deposition Author(s): Vorobiev, S.M., Su, M., Seetharaman, J., Benach, J., Forouhar, F., Clayton, G., Cooper, B., Wang, H., Foote, E.L., Ciccosanti, C., Mao, L., Xiao, R., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2008-10-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary