3CFU

Crystal structure of the yjhA protein from Bacillus subtilis. Northeast Structural Genomics Consortium target SR562

• PDB DOI: https://doi.org/10.2210/pdb3CFU/pdb

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


• Deposited: 2008-03-04 Released: 2008-03-18 
• Deposition Author(s): Vorobiev, S.M., Chen, Y., Kuzin, A.P., Seetharaman, J., Forouhar, F., Zhao, L., Mao, L., Maglaqui, M., Xiao, R., Liu, J., Swapna, G., Huang, J.Y., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.254 
• R-Value Work: 0.231 
• R-Value Observed: 0.231 

Literature

Crystal structure of the yjhA protein from Bacillus subtilis.

Vorobiev, S.M., Chen, Y., Kuzin, A.P., Seetharaman, J., Forouhar, F., Zhao, L., Mao, L., Maglaqui, M., Xiao, R., Liu, J., Swapna, G., Huang, J.Y., 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: 36.7 kDa 
• Atom Count: 2,237 
• Modelled Residue Count: 280 
• Deposited Residue Count: 318 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized lipoprotein yjhA	A, B	159	Bacillus subtilis	Mutation(s): 0  Gene Names: yjhA, BSU12180
UniProt
Find proteins for O34725 (Bacillus subtilis (strain 168)) Explore O34725  Go to UniProtKB:  O34725

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: 2.40 Å
• R-Value Free: 0.254 
• R-Value Work: 0.231 
• R-Value Observed: 0.231 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.678	α = 90
b = 41.687	β = 91.74
c = 65.656	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
SnB	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-18 
Deposition Author(s): Vorobiev, S.M., Chen, Y., Kuzin, A.P., Seetharaman, J., Forouhar, F., Zhao, L., Mao, L., Maglaqui, M., Xiao, R., Liu, J., Swapna, G., Huang, J.Y., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2008-03-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary