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.

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)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1074/jbc.M114.565879
Primary Citation of 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.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8ZQ08
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-05-14

Deposition Author(s):

King, D.T.

Strynadka, N.C.J.

Revision History (Full details and data files)

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