Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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

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

Macromolecule Content

• Total Structure Weight: 30.88 kDa 
• Atom Count: 2269 
• Modelled Residue Count: 251 
• Deposited Residue Count: 261 
• Unique protein chains: 1

3QKY

Crystal structure of Rhodothermus marinus BamD

• PDB DOI: 10.2210/pdb3QKY/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Rhodothermus marinus DSM 4252
• Mutation(s): No 


• Deposited: 2011-02-02 Released: 2011-04-20 
• Deposition Author(s): Sandoval, C.M., Baker, S.L., Jansen, K., Metzner, S.I., Sousa, M.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.210 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 

Literature

Crystal Structure of BamD. An Essential Component of the beta-Barrel Assembly Machinery of Gram Negative Bacteria

Sandoval, C.M., Baker, S.L., Jansen, K., Metzner, S.I., Sousa, M.C.

(2011) J Mol Biol 

• PubMed: 21463635 
• DOI: 10.1016/j.jmb.2011.03.035
• Primary Citation of Related Structures:  
  3QKY


• PubMed Abstract: 
  

Folding and insertion of integral β-barrel proteins in the outer membrane (OM) is an essential process for Gram-negative bacteria that requires the β-barrel assembly machinery (BAM). Efficient OM protein (OMP) folding and insertion appears to require a consensus C-terminal signal in OMPs characterized by terminal F or W residues. The BAM complex is embedded in the OM and, in Escherichia coli, consists of the β-barrel BamA and four lipoproteins BamBCDE. BamA and BamD are broadly distributed across all species of Gram-negative bacteria, whereas the other components are present in only a subset of species. BamA and BamD are also essential for viability, suggesting that these two proteins constitute the functional core of the bacterial BAM complex. Here, we present the crystal structure of BamD from the thermophilic bacteria Rhodothermus marinus refined to 2.15 Å resolution. The protein contains five tetratricopeptide repeats (TPRs) organized into two offset tandems, each capped by a terminal helix. The N-terminal domain contains three TPRs and displays remarkable structural similarity with proteins that recognize targeting signals in extended conformations. The C-terminal domain harbors the remaining two TPRs and previously described mutations that impair binding to other BAM components map to this domain. Therefore, the structure suggests a model where the C-terminal domain provides a scaffold for interaction with BAM components, while the N-terminal domain participates in interaction with the substrates, either recognizing the C-terminal consensus sequence or binding unfolded OMP intermediates.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of Colorado at Boulder, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane assembly lipoprotein YfiO	A	261	Rhodothermus marinus DSM 4252	Mutation(s): 0  Gene Names: Rmar_0679
UniProt
Find proteins for D0MFQ0 (Rhodothermus marinus (strain ATCC 43812 / DSM 4252 / R-10)) Explore D0MFQ0  Go to UniProtKB:  D0MFQ0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.210 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.37	α = 90
b = 114.37	β = 90
c = 77.63	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-02-02 
• Released Date: 2011-04-20 
Deposition Author(s): Sandoval, C.M., Baker, S.L., Jansen, K., Metzner, S.I., Sousa, M.C.

Revision History  

• Version 1.0: 2011-04-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-11-16
  Changes: Atomic model