3Q54

Crystal structure of Escherichia coli BamB

PDB DOI: https://doi.org/10.2210/pdb3Q54/pdb

Classification: LIPID BINDING PROTEIN
Organism(s): Escherichia coli DH1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-12-27 Released: 2012-05-09
Deposition Author(s): Dong, C., Hou, H., Yang, X.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.232
R-Value Work: 0.172
R-Value Observed: 0.175

wwPDB Validation 3D Report Full Report

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

Literature

Structure of Escherichia coli BamB and its interaction with POTRA domains of BamA.

Dong, C., Yang, X., Hou, H.F., Shen, Y.Q., Dong, Y.H.

(2012) Acta Crystallogr D Biol Crystallogr 68: 1134-1139

PubMed: 22948914 Search on PubMed
DOI: https://doi.org/10.1107/S0907444912023141
Primary Citation of Related Structures:
3Q54

PubMed Abstract:
In Escherichia coli, the BAM complex is essential for the assembly and insertion of outer membrane proteins (OMPs). The BAM complex is comprised of an integral β-barrel outer membrane protein BamA and four accessory lipoproteins BamB, BamC, BamD and BamE. Here, the crystal structure of BamB is reported. The crystal of BamB diffracted to 2.0 Å with one monomer in the asymmetric unit and the structure is composed of eight-bladed β-propeller motifs. Pull-down and Western blotting assays indicate that BamB interacts directly with the POTRA 1-3 domain of BamA and the C-terminal region of the POTRA 1-3 domain plays an important role in the interaction, while the POTRA 1-2 domain is not required for the interaction.

Organizational Affiliation

State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, People's Republic of China.

Macromolecule Content

Total Structure Weight: 39.32 kDa
Atom Count: 2,968
Modelled Residue Count: 349
Deposited Residue Count: 368
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane assembly lipoprotein YfgL	A	368	Escherichia coli DH1	Mutation(s): 0 Gene Names: EcDH1_1156
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.232
R-Value Work: 0.172
R-Value Observed: 0.175
Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.15	α = 90
b = 121.123	β = 90
c = 133.294	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
SHELXS	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-05-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-05-09
Type: Initial release
Version 1.1: 2012-09-19
Changes: Database references
Version 1.2: 2024-02-21
Changes: Data collection, 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.