2EUC

Crystal structure of YfmB from Bacillus subtilis. NESG TARGET SR324

• PDB DOI: https://doi.org/10.2210/pdb2EUC/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-10-28 Released: 2005-11-08 
• Deposition Author(s): Benach, J., Abashidze, M., Jayaraman, S., Janjua, H., Cooper, B., Rong, X., 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: 2.50 Å
• R-Value Free: 0.328 
• R-Value Work: 0.274 
• R-Value Observed: 0.274 

Literature

Crystal structure of YfmB from bacillus subtilis NESG TARGET SR324.

Benach, J., Abashidze, M., Jayaraman, S., Rong, X., Acton, T.B., Montelione, G.T., Tong, L.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 30.62 kDa 
• Atom Count: 1,960 
• Modelled Residue Count: 216 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein yfmB	A, B	130	Bacillus subtilis	Mutation(s): 4  Gene Names: yfmB
UniProt
Find proteins for O34626 (Bacillus subtilis (strain 168)) Explore O34626  Go to UniProtKB:  O34626

Small Molecules

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: 2.50 Å
• R-Value Free: 0.328 
• R-Value Work: 0.274 
• R-Value Observed: 0.274 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.543	α = 90
b = 67.637	β = 90
c = 78.015	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	model building
CNS	refinement
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-11-08 
Deposition Author(s): Benach, J., Abashidze, M., Jayaraman, S., Janjua, H., Cooper, B., Rong, X., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2005-11-08
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary