4WJT

Stationary Phase Survival Protein YuiC from B.subtilis complexed with NAG

• PDB DOI: https://doi.org/10.2210/pdb4WJT/pdb

• Classification: LYASE
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-10-01 Released: 2015-07-08 
• Deposition Author(s): Quay, D.H.X., Cole, A.R., Cryar, A., Thalassinos, K., Williams, M.A., Bhakta, S., Keep, N.H.
• Funding Organization(s): Commonwealth Studies Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.21 Å
• R-Value Free: 0.144 
• R-Value Work: 0.111 
• R-Value Observed: 0.112 

Literature

Structure of the stationary phase survival protein YuiC from B.subtilis.

Quay, D.H., Cole, A.R., Cryar, A., Thalassinos, K., Williams, M.A., Bhakta, S., Keep, N.H.

(2015) BMC Struct Biol 15: 12-12

• PubMed: 26163297 
• DOI: https://doi.org/10.1186/s12900-015-0039-z
• Primary Citation of Related Structures:  
  4WJT, 4WLI, 4WLK


• PubMed Abstract: 
  

  Stationary phase survival proteins (Sps) were found in Firmicutes as having analogous domain compositions, and in some cases genome context, as the resuscitation promoting factors of Actinobacteria, but with a different putative peptidoglycan cleaving domain.

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Organizational Affiliation: 

Institute for Structural and Molecular Biology, Crystallography, Department of Biological Sciences, Birkbeck University of London, Malet Street, London, WC1E 7HX, UK. [e-mail].

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: 38.16 kDa 
• Atom Count: 2,815 
• Modelled Residue Count: 292 
• Deposited Residue Count: 334 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein YuiC	A, B	167	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  Gene Names: yuiC, BSU32070
UniProt
Find proteins for O32108 (Bacillus subtilis (strain 168)) Explore O32108  Go to UniProtKB:  O32108

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A], E [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
3P9	F [auth B]	(2S)-2-{[(2S)-2-{[(2R)-2-hydroxypropyl]oxy}propyl]oxy}propan-1-ol C9 H20 O4 LCZVSXRMYJUNFX-VGMNWLOBSA-N
DMS	D [auth A], G [auth B], H [auth B], I [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.21 Å
• R-Value Free: 0.144 
• R-Value Work: 0.111 
• R-Value Observed: 0.112 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.48	α = 90
b = 145.48	β = 90
c = 37.82	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
ACORN	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-07-08 
Deposition Author(s): Quay, D.H.X., Cole, A.R., Cryar, A., Thalassinos, K., Williams, M.A., Bhakta, S., Keep, N.H.

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Funding Organization	Location	Grant Number
Commonwealth Studies Commission	United Kingdom	MYCS-2011-252

Revision History  

• Version 1.0: 2015-07-08
  Type: Initial release
  
• Version 1.1: 2016-09-21
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Refinement description, Structure summary