2IEE

Crystal Structure of YCKB_BACSU from Bacillus subtilis. Northeast Structural Genomics Consortium target SR574.

• PDB DOI: https://doi.org/10.2210/pdb2IEE/pdb

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


• Deposited: 2006-09-18 Released: 2006-10-03 
• Deposition Author(s): Kuzin, A.P., Su, M., Jayaraman, S., Chen, X.C., Jang, M., Cunningham, K., Ma, C., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.241 
• R-Value Work: 0.202 
• R-Value Observed: 0.202 

Literature

Crystal structure of probable ABC transporter extracellular-binding protein yckB from Bacillus subtilis.

Kuzin, A.P., Su, M., Seetharaman, J., Chen, X.C., Jang, M., Cunningham, K., Ma, L.C., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 61.03 kDa 
• Atom Count: 4,048 
• Modelled Residue Count: 495 
• Deposited Residue Count: 542 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable ABC transporter extracellular-binding protein yckB	A, B	271	Bacillus subtilis	Mutation(s): 7  Gene Names: yckB
UniProt
Find proteins for P42400 (Bacillus subtilis (strain 168)) Explore P42400  Go to UniProtKB:  P42400

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: 2.20 Å
• R-Value Free: 0.241 
• R-Value Work: 0.202 
• R-Value Observed: 0.202 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.284	α = 90
b = 49.918	β = 99.73
c = 106.768	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
SnB	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-03 
Deposition Author(s): Kuzin, A.P., Su, M., Jayaraman, S., Chen, X.C., Jang, M., Cunningham, K., Ma, C., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2006-10-03
  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: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary