8H1S | pdb_00008h1s

Crystal structure of apo-LptDE complex

PDB DOI: https://doi.org/10.2210/pdb8H1S/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Pseudomonas aeruginosa PAO1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-10-03 Released: 2023-10-11
Deposition Author(s): Luo, Q., Huang, Y.
Funding Organization(s): Chinese Academy of Sciences, National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.28 Å
R-Value Free:
0.279 (Depositor), 0.280 (DCC)
R-Value Work:
0.242 (Depositor), 0.240 (DCC)
R-Value Observed:
0.244 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Surface lipoprotein sorting by crosstalk between Lpt and Lol pathways in gram-negative bacteria

Luo, Q., Wang, C., Qiao, S., Yu, S., Chen, L., Kim, S., Wang, K., Zheng, J., Zhang, Y., Wu, F., Lei, X., Lou, J., Hennig, M., Im, W., Miao, L., Zhou, M., Bei, W., Huang, Y.

(2025) Nat Commun 16: 4357

DOI: https://doi.org/10.1038/s41467-025-59660-y

Macromolecule Content

Total Structure Weight: 254.59 kDa
Atom Count: 15,855
Modeled Residue Count: 1,981
Deposited Residue Count: 2,262
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LPS-assembly protein LptD	A [auth C], C [auth A]	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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9I5U2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LPS-assembly lipoprotein LptE	B [auth D], D [auth B]	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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9HX32
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.28 Å
R-Value Free: 0.279 (Depositor), 0.280 (DCC)
R-Value Work: 0.242 (Depositor), 0.240 (DCC)
R-Value Observed: 0.244 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.027	α = 90
b = 160.485	β = 90
c = 218.075	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-10-11

Deposition Author(s):

Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	CAS201973
Chinese Academy of Sciences	China	XDB37020201
National Natural Science Foundation of China (NSFC)	China	31625009

Revision History (Full details and data files)

Version 1.0: 2023-10-11
Type: Initial release
Version 1.1: 2024-11-20
Changes: Structure summary
Version 1.2: 2025-05-21
Changes: Database references

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.