2O1M

Crystal structure of the probable amino-acid ABC transporter extracellular-binding protein ytmK from Bacillus subtilis. Northeast Structural Genomics Consortium target SR572

• PDB DOI: https://doi.org/10.2210/pdb2O1M/pdb

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


• Deposited: 2006-11-29 Released: 2006-12-19 
• Deposition Author(s): Kuzin, A.P., Su, M., Seetharaman, J., Chen, C.X., Fang, Y., Cunningham, K., Ma, L.C., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.264 
• R-Value Work: 0.230 
• R-Value Observed: 0.230 

Literature

Crystal structure of the probable amino-acid ABC transporter extracellular-binding protein ytmK from Bacillus subtilis. Northeast Structural Genomics Consortium target SR572.

Kuzin, A.P., Su, M., Seetharaman, J., Chen, C., Fang, Y., 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: 59.18 kDa 
• Atom Count: 3,969 
• Modelled Residue Count: 456 
• Deposited Residue Count: 516 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable amino-acid ABC transporter extracellular-binding protein ytmK	A, B	258	Bacillus subtilis	Mutation(s): 3  Gene Names: ytmK
UniProt
Find proteins for O34852 (Bacillus subtilis (strain 168)) Explore O34852  Go to UniProtKB:  O34852

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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: 2.00 Å
• R-Value Free: 0.264 
• R-Value Work: 0.230 
• R-Value Observed: 0.230 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.563	α = 90
b = 88.931	β = 90
c = 76.697	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: 2006-12-19 
Deposition Author(s): Kuzin, A.P., Su, M., Seetharaman, J., Chen, C.X., Fang, Y., Cunningham, K., Ma, L.C., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2006-12-19
  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: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2024-10-16
  Changes: Structure summary