2J5Y | pdb_00002j5y

Crystal structure of the GA module from F.magna

• PDB DOI: https://doi.org/10.2210/pdb2J5Y/pdb

• Classification: PROTEIN BINDING
• Organism(s): Finegoldia magna
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-09-20 Released: 2007-06-26 
• Deposition Author(s): Lejon, S., Cramer, J.F., Nordberg, P.A., Lundqvist, T., Valegard, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.199 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.146 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of a Bacterial Albumin-Binding Domain at 1.4A Resolution.

Cramer, J.F., Nordberg, P.A., Hajdu, J., Lejon, S.

(2007) FEBS Lett 581: 3178

• PubMed: 17575979 
• DOI: https://doi.org/10.1016/j.febslet.2007.06.003
• Primary Citation Related Structures: 
  2J5Y


• PubMed Abstract: 
  

  The albumin-binding domain, or GA module, of the peptostreptococcal albumin-binding protein expressed in pathogenic strains of Finegoldia magna is believed to be responsible for the virulence and increased growth rate of these strains. Here we present the 1.4A crystal structure of this domain, and compare it with the crystal structure of the GA-albumin complex. An analysis of protein-protein interactions in the two crystals, and the presence of multimeric GA species in solution, indicate the GA module is "sticky", and is capable of forming contacts with a range of protein surfaces. This might lead to interactions with different host proteins.

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Organizational Affiliation: 
• Department of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Uppsala, Sweden.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 13.64 kDa 
• Atom Count: 1,221 
• Modeled Residue Count: 122 
• Deposited Residue Count: 122 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPTOSTREPTOCOCCAL ALBUMIN-BINDING PROTEIN	A, B	61	Finegoldia magna	Mutation(s): 0
UniProt
Find proteins for Q51911 (Finegoldia magna) Explore Q51911  Go to UniProtKB:  Q51911

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.199 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.146 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.784	α = 90
b = 58.068	β = 90.03
c = 40.57	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-26 
Deposition Author(s): Lejon, S., Cramer, J.F., Nordberg, P.A., Lundqvist, T., Valegard, K.

Revision History  

• Version 1.0: 2007-06-26
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description