2IKK | pdb_00002ikk

Structural Genomics, the crystal structure of the C-terminal domain of Yurk from Bacillus subtilis subsp. subtilis str. 168

• PDB DOI: https://doi.org/10.2210/pdb2IKK/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2006-10-02 Released: 2006-10-31 
• Deposition Author(s): Tan, K., Hatzos, C., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.230 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Literature

The crystal structure of the C-terminal domain of Yurk from Bacillus subtilis subsp. subtilis str. 168

Tan, K., Hatzos, C., Abdullah, J., Joachimiak, A.

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)

Macromolecule Content 

• Total Structure Weight: 39.98 kDa 
• Atom Count: 2,548 
• Modeled Residue Count: 291 
• Deposited Residue Count: 346 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical transcriptional regulator yurK	A, B	173	Bacillus subtilis	Mutation(s): 2
UniProt
Find proteins for O32152 (Bacillus subtilis (strain 168)) Explore O32152  Go to UniProtKB:  O32152

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [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: 1.80 Å
• R-Value Free:  0.230 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.509	α = 90
b = 104.704	β = 118.58
c = 40.538	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data reduction
HKL-2000	data scaling
HKL-3000	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-31 
Deposition Author(s): Tan, K., Hatzos, C., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2006-10-31
  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: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary