3KB2

Crystal Structure of YorR protein in complex with phosphorylated GDP from Bacillus subtilis, Northeast Structural Genomics Consortium Target SR256

• PDB DOI: https://doi.org/10.2210/pdb3KB2/pdb

• Classification: structural genomics, unknown function
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-10-20 Released: 2009-10-27 
• Deposition Author(s): Forouhar, F., Friedman, D., Seetharaman, J., Janjua, J., Xiao, R., Cunningham, K., Ma, L., Ho, C., Everett, J.K., Nair, R., 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: 0.262 
• R-Value Work: 0.195 
• R-Value Observed: 0.196 

Literature

Northeast Structural Genomics Consortium Target SR256

Forouhar, F., Friedman, D., Seetharaman, J., Janjua, J., Xiao, R., Cunningham, K., Ma, L., Ho, C., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F.

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.

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 41.61 kDa 
• Atom Count: 3,018 
• Modelled Residue Count: 338 
• Deposited Residue Count: 346 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SPBc2 prophage-derived uncharacterized protein yorR	A, B	173	Bacillus subtilis	Mutation(s): 0  Gene Names: BSU20280, yorR
UniProt
Find proteins for O31896 (Bacillus subtilis (strain 168)) Explore O31896  Go to UniProtKB:  O31896

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G3D	C [auth A], E [auth B]	GUANOSINE-3'-MONOPHOSPHATE-5'-DIPHOSPHATE C10 H16 N5 O14 P3 HEYSFDAMRDTCJM-UUOKFMHZSA-N
MG	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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: 0.262 
• R-Value Work: 0.195 
• R-Value Observed: 0.196 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.478	α = 90
b = 63.05	β = 91.57
c = 70.456	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-27 
Deposition Author(s): Forouhar, F., Friedman, D., Seetharaman, J., Janjua, J., Xiao, R., Cunningham, K., Ma, L., Ho, C., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2009-10-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description