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.

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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 

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 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

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

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

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

Entry History 

Deposition Data

• Released Date: 2012-05-09 
Deposition Author(s): Dong, C., Hou, H., Yang, X.

Revision History  

• 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