8H1R

Crystal structure of LptDE-YifL complex

• PDB DOI: https://doi.org/10.2210/pdb8H1R/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Pseudomonas aeruginosa PAO1, Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-10-03 Released: 2023-10-25 
• Deposition Author(s): Luo, Q., Huang, Y.
• Funding Organization(s): Ministry of Science and Technology (MoST, China), Chinese Academy of Sciences, National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.98 Å
• R-Value Free: 0.264 
• R-Value Work: 0.234 
• R-Value Observed: 0.235 

Literature

Lipoprotein sorting to the cell surface via a crosstalk between the Lpt and Lol pathways during outer membrane biogenesis

Luo, Q., Wang, C., Qiao, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Macromolecule Content

• Total Structure Weight: 270.75 kDa 
• Atom Count: 15,349 
• Modelled Residue Count: 1,893 
• Deposited Residue Count: 2,396 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LPS-assembly protein LptD	A, D	924	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: lptD, imp, ostA, PA0595
UniProt
Find proteins for Q9I5U2 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I5U2  Go to UniProtKB:  Q9I5U2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LPS-assembly lipoprotein LptE	B, E	207	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: lptE, PA3988
UniProt
Find proteins for Q9HX32 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HX32  Go to UniProtKB:  Q9HX32

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized lipoprotein YifL	C, F	67	Escherichia coli K-12	Mutation(s): 0  Gene Names: yifL, b4558, JW3781
UniProt
Find proteins for P0ADN6 (Escherichia coli (strain K12)) Explore P0ADN6  Go to UniProtKB:  P0ADN6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PCJ (Subject of Investigation/LOI)	G [auth A], H [auth D]	(2R)-3-{[(2S)-3-HYDROXY-2-(PALMITOYLAMINO)PROPYL]THIO}PROPANE-1,2-DIYL DIHEXADECANOATE C54 H105 N O6 S GBQDHEZHWNJSLG-OKPYTHRESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.98 Å
• R-Value Free: 0.264 
• R-Value Work: 0.234 
• R-Value Observed: 0.235 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.848	α = 90
b = 140.475	β = 104.39
c = 133.18	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-10-25 
Deposition Author(s): Luo, Q., Huang, Y.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2016YFA0500404
Chinese Academy of Sciences	China	XDB37020201
National Natural Science Foundation of China (NSFC)	China	31625009

Revision History  

• Version 1.0: 2023-10-25
  Type: Initial release