4Q6V | pdb_00004q6v

LpoB C-terminal domain from Salmonella enterica (Sel-Met)

• PDB DOI: https://doi.org/10.2210/pdb4Q6V/pdb

• Classification: PROTEIN BINDING
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-04-23 Released: 2014-05-14 
• Deposition Author(s): King, D.T., Strynadka, N.C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 
  0.290 (Depositor), 0.293 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.233 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Literature

Structural Insights into the Lipoprotein Outer Membrane Regulator of Penicillin-binding Protein 1B.

King, D.T., Lameignere, E., Strynadka, N.C.

(2014) J Biological Chem 289: 19245-19253

• PubMed: 24808177 
• DOI: https://doi.org/10.1074/jbc.M114.565879
• Primary Citation Related Structures: 
  4Q6L, 4Q6V, 4Q6Z


• PubMed Abstract: 
  

  In bacteria, the synthesis of the protective peptidoglycan sacculus is a dynamic process that is tightly regulated at multiple levels. Recently, the lipoprotein co-factor LpoB has been found essential for the in vivo function of the major peptidoglycan synthase PBP1b in Enterobacteriaceae. Here, we reveal the crystal structures of Salmonella enterica and Escherichia coli LpoB. The LpoB protein can be modeled as a ball and tether, consisting of a disordered N-terminal region followed by a compact globular C-terminal domain. Taken together, our structural data allow us to propose new insights into LpoB-mediated regulation of peptidoglycan synthesis.

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Organizational Affiliation: 
• From the Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.
From the Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 14.59 kDa 
• Atom Count: 1,022 
• Modeled Residue Count: 135 
• Deposited Residue Count: 136 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Penicillin-binding protein activator LpoB	A	136	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0  Gene Names: lpoB, STM1207
UniProt
Find proteins for Q8ZQ08 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZQ08  Go to UniProtKB:  Q8ZQ08

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free:  0.290 (Depositor), 0.293 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.233 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.35	α = 90
b = 37.93	β = 90
c = 98.59	γ = 90

Software Package:

Software Name	Purpose
MxDC	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-05-14 
Deposition Author(s): King, D.T., Strynadka, N.C.J.

Revision History  

• Version 1.0: 2014-05-14
  Type: Initial release
  
• Version 1.1: 2014-07-02
  Changes: Database references
• Version 1.2: 2014-07-23
  Changes: Database references
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary