3Q5M

Crystal structure of Escherichia coli BamD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.604 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of Escherichia coli BamD and its functional implications in outer membrane protein assembly

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

(2012) Acta Crystallogr.,Sect.D 68: 95-101

  • DOI: 10.1107/S0907444911051031

  • PubMed Abstract: 
  • The outer membrane protein complex (BAM complex) plays an important role in outer membrane protein (OMP) assembly in Escherichia coli. The BAM complex includes the integral β-barrel protein BamA as well as four lipoproteins: BamB, BamC, BamD and BamE ...

    The outer membrane protein complex (BAM complex) plays an important role in outer membrane protein (OMP) assembly in Escherichia coli. The BAM complex includes the integral β-barrel protein BamA as well as four lipoproteins: BamB, BamC, BamD and BamE. One of these lipoproteins, BamD, is essential for the survival of Escherichia coli. The structure of BamD at 2.6 Å resolution shows that this lipoprotein is composed of ten α-helices that form five tetratricopeptide-repeat (TPR) motifs. The arrangement of the BamD motifs is similar to that in the periplasmic part of BamA. One of the ten α-helices, α10, which has been shown to be important for the assembly of the BAM complex, is located in the very C-terminal region of BamD. A deep groove between TPR domains 4 and 5 is also observed. This groove, as well as the surface around α10, may provide binding sites for other components of the BAM complex. The C-terminal region of BamD serves as a platform for interactions with other components of the BAM complex. The N-terminal region shares structural similarity to other proteins whose functions are related to assistance in or regulation of secretion. Therefore, this region is likely to play an important role in the insertion of other outer membrane proteins.


    Organizational Affiliation

    Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UPF0169 lipoprotein yfiO
A
224Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: bamD (yfiO)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL
Sub Group: 
Omp85-TpsB Outer Membrane Transporter Superfamily
Protein: 
BamD component of the Bam β-barrel assembly machine
Find proteins for P0AC02 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AC02
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download SDF File 
Download CCD File 
A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.604 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.216 
  • Space Group: P 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 106.549α = 90.00
b = 106.549β = 90.00
c = 65.070γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-28
    Type: Initial release
  • Version 1.1: 2012-02-01
    Type: Database references
  • Version 1.2: 2012-05-02
    Type: Database references