4FIB

Crystal structure of the ydhK protein from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR518A.

• PDB DOI: https://doi.org/10.2210/pdb4FIB/pdb

• Classification: Structural Genomics, Unknown Function
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-06-08 Released: 2012-06-20 
• Deposition Author(s): Vorobiev, S., Abashidze, M., Seetharaman, J., Mao, M., Xiao, R., Maglaqui, M., Owens, L.A., Cunningham, K., Zhao, L., Everett, J.K., Acton, T.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: 2.00 Å
• R-Value Free: 0.255 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 

Literature

Crystal structure of the ydhK protein from Bacillus subtilis.

Vorobiev, S., Abashidze, M., Seetharaman, J., Mao, M., Xiao, R., Maglaqui, M., Owens, L.A., Cunningham, K., Zhao, L., Everett, J.K., Acton, T.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 and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43.82 kDa 
• Atom Count: 2,997 
• Modelled Residue Count: 372 
• Deposited Residue Count: 387 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein ydhK	A, B, C	129	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  Gene Names: BSU05790, ydhK
UniProt
Find proteins for O05503 (Bacillus subtilis (strain 168)) Explore O05503  Go to UniProtKB:  O05503

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: 2.00 Å
• R-Value Free: 0.255 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.861	α = 90
b = 69.493	β = 113.94
c = 61.487	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXDE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-20 
Deposition Author(s): Vorobiev, S., Abashidze, M., Seetharaman, J., Mao, M., Xiao, R., Maglaqui, M., Owens, L.A., Cunningham, K., Zhao, L., Everett, J.K., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2012-06-20
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary