4RHB | pdb_00004rhb

Crystal structure of the lipopolysaccharide assembly complex LptD-LptE from the Escherichia coli outer membrane

• PDB DOI: https://doi.org/10.2210/pdb4RHB/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMD


• Deposited: 2014-10-01 Released: 2015-08-26 
• Deposition Author(s): Malojcic, G., Garner, R.A., Kahne, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.35 Å
• R-Value Free: 
  0.338 (Depositor), 0.332 (DCC) 
• R-Value Work: 
  0.257 (Depositor), 0.258 (DCC) 
• R-Value Observed: 
  0.261 (Depositor) 

Starting Model: experimental

Literature

Structural basis of lipopolysaccharide insertion into the bacterial outer membrane

Malojcic, G., Garner, R.A., Kahne, D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 181.59 kDa 
• Atom Count: 11,615 
• Modeled Residue Count: 1,413 
• Deposited Residue Count: 1,578 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LPS-assembly protein LptD	A, C	614	Escherichia coli K-12	Mutation(s): 0  Gene Names: lptD, imp, ostA, yabG, b0054, JW0053 Membrane Entity: Yes
UniProt
Find proteins for P31554 (Escherichia coli (strain K12)) Explore P31554  Go to UniProtKB:  P31554

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LPS-assembly lipoprotein LptE	B, D	175	Escherichia coli K-12	Mutation(s): 0  Gene Names: lptE, rlpB, b0641, JW0636 Membrane Entity: Yes
UniProt
Find proteins for P0ADC1 (Escherichia coli (strain K12)) Explore P0ADC1  Go to UniProtKB:  P0ADC1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	E [auth A], G [auth C], H [auth C], I [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.35 Å
• R-Value Free:  0.338 (Depositor), 0.332 (DCC) 
• R-Value Work:  0.257 (Depositor), 0.258 (DCC) 
• R-Value Observed: 0.261 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.04	α = 90
b = 136.62	β = 90
c = 108.31	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-08-26 
Deposition Author(s): Malojcic, G., Garner, R.A., Kahne, D.

Revision History  

• Version 1.0: 2015-08-26
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description