4RH8 | pdb_00004rh8

Crystal structure of the outer membrane lipopolysaccharide transport protein LptE (RlpB) from Escherichia coli in the tetragonal crystal form

PDB DOI: https://doi.org/10.2210/pdb4RH8/pdb

Classification: LIPID BINDING PROTEIN
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2014-10-01 Released: 2015-11-11
Deposition Author(s): Malojcic, G., Kahne, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.262 (Depositor), 0.266 (DCC)
R-Value Work:
0.225 (Depositor), 0.229 (DCC)
R-Value Observed:
0.227 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Structural basis of lipopolysaccharide insertion into the bacterial outer membrane

Malojcic, G., Kahne, D.

To be published.

Macromolecule Content

Total Structure Weight: 75.68 kDa
Atom Count: 4,376
Modeled Residue Count: 534
Deposited Residue Count: 672
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LPS-assembly lipoprotein LptE	A, B, C, D	168	Escherichia coli K-12	Mutation(s): 3 Gene Names: lptE, rlpB, b0641, JW0636
UniProt
Find proteins for P0ADC1 (Escherichia coli (strain K12)) Explore P0ADC1 Go to UniProtKB: P0ADC1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0ADC1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth D] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth D] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth C], H [auth D]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.262 (Depositor), 0.266 (DCC)
R-Value Work: 0.225 (Depositor), 0.229 (DCC)
R-Value Observed: 0.227 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.46	α = 90
b = 102.46	β = 90
c = 166.84	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
Aimless	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-11-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-11-11
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.