4WJT

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


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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


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

  • DOI: 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 ...

    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.


    Organizational Affiliation

    Institute for Structural and Molecular Biology, Crystallography, Department of Biological Sciences, Birkbeck University of London, Malet Street, London, WC1E 7HX, UK. n.keep@mail.cryst.bbk.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized protein YuiCA, B167Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: yuiCBSU32070
UniProt
Find proteins for O32108 (Bacillus subtilis (strain 168))
Explore O32108 
Go to UniProtKB:  O32108
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO32108
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
3P9
Query on 3P9

Download Ideal Coordinates CCD File 
F [auth B](2S)-2-{[(2S)-2-{[(2R)-2-hydroxypropyl]oxy}propyl]oxy}propan-1-ol
C9 H20 O4
LCZVSXRMYJUNFX-VGMNWLOBSA-N
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B],
H [auth B],
I [auth B]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
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 = 145.48α = 90
b = 145.48β = 90
c = 37.82γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
ACORNphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Commonwealth Studies CommissionUnited KingdomMYCS-2011-252

Revision History  (Full details and data files)

  • 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