4XGA

Crystal structure of BamB and BamA P3-5 complex from E.coli

• PDB DOI: https://doi.org/10.2210/pdb4XGA/pdb

• Classification: PROTEIN BINDING/MEMBRANE PROTEIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  OPMmpstruc


• Deposited: 2014-12-30 Released: 2016-01-20 
• Deposition Author(s): Chen, Z., Zhan, L.H., Dong, C., Gao, Z.Q., Dong, Y.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.231 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 

Starting Models: experimental

Literature

Structural basis for the interaction of BamB with the POTRA3-4 domains of BamA.

Chen, Z., Zhan, L.H., Hou, H.F., Gao, Z.Q., Xu, J.H., Dong, C., Dong, Y.H.

(2016) Acta Crystallogr D Struct Biol 72: 236-244

• PubMed: 26894671 
• DOI: https://doi.org/10.1107/S2059798315024729
• Primary Citation of Related Structures:  
  4XGA


• PubMed Abstract: 
  

  In Escherichia coli, the Omp85 protein BamA and four lipoproteins (BamBCDE) constitute the BAM complex, which is essential for the assembly and insertion of outer membrane proteins into the outer membrane. Here, the crystal structure of BamB in complex with the POTRA3-4 domains of BamA is reported at 2.1 Å resolution. Based on this structure, the POTRA3 domain is associated with BamB via hydrogen-bonding and hydrophobic interactions. Structural and biochemical analysis revealed that the conserved residues Arg77, Glu127, Glu150, Ser167, Leu192, Leu194 and Arg195 of BamB play an essential role in interaction with the POTRA3 domain.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 68.06 kDa 
• Atom Count: 4,283 
• Modelled Residue Count: 521 
• Deposited Residue Count: 619 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane protein assembly factor BamB	A	373	Escherichia coli K-12	Mutation(s): 0  Gene Names: bamB, yfgL, b2512, JW2496 Membrane Entity: Yes
UniProt
Find proteins for P77774 (Escherichia coli (strain K12)) Explore P77774  Go to UniProtKB:  P77774

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane protein assembly factor BamA	B	246	Escherichia coli K-12	Mutation(s): 0  Gene Names: bamA, yaeT, yzzN, yzzY, b0177, JW0172 Membrane Entity: Yes
UniProt
Find proteins for P0A940 (Escherichia coli (strain K12)) Explore P0A940  Go to UniProtKB:  P0A940

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.231 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.035	α = 90
b = 109.642	β = 90
c = 49.488	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-20 
Deposition Author(s): Chen, Z., Zhan, L.H., Dong, C., Gao, Z.Q., Dong, Y.H.

Revision History  

• Version 1.0: 2016-01-20
  Type: Initial release
  
• Version 1.1: 2016-03-09
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description