2I2L

X-ray Crystal Structure of Protein yopX from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR411.

• PDB DOI: https://doi.org/10.2210/pdb2I2L/pdb

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


• Deposited: 2006-08-16 Released: 2006-08-29 
• Deposition Author(s): Vorobiev, S.M., Zhou, W., Seetharaman, J., Forouhar, F., Kuzin, A.A., Ho, C.K., Janjua, H., Cunningham, K., Ma, L.C., Xiao, R., Liu, J., Acton, T., 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: 2.80 Å
• R-Value Free: 0.286 
• R-Value Work: 0.241 
• R-Value Observed: 0.241 

Literature

Crystal structure of the hypothetical protein yopX from Bacillus subtilis

Vorobiev, S.M., Zhou, W., Seetharaman, J., Forouhar, F., Kuzin, A.A., Ho, C.K., Cunningham, K., Ma, L.C., Xiao, R., Liu, J., Acton, T., Montelione, G.T., Hunt, J.F., 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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 49.26 kDa 
• Atom Count: 3,102 
• Modelled Residue Count: 391 
• Deposited Residue Count: 426 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YopX protein	A, B, C	142	Bacillus subtilis	Mutation(s): 3  Gene Names: yopX
UniProt
Find proteins for O34401 (Bacillus subtilis (strain 168)) Explore O34401  Go to UniProtKB:  O34401

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.286 
• R-Value Work: 0.241 
• R-Value Observed: 0.241 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.521	α = 90
b = 99.521	β = 90
c = 87.43	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
SHELXD	phasing
SHELXE	model building
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-08-29 
Deposition Author(s): Vorobiev, S.M., Zhou, W., Seetharaman, J., Forouhar, F., Kuzin, A.A., Ho, C.K., Janjua, H., Cunningham, K., Ma, L.C., Xiao, R., Liu, J., Acton, T., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2006-08-29
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance