4PZ0 | pdb_00004pz0

The crystal structure of a solute binding protein from Bacillus anthracis str. Ames in complex with quorum-sensing signal autoinducer-2 (AI-2)

• PDB DOI: https://doi.org/10.2210/pdb4PZ0/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Bacillus anthracis str. Ames
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-03-28 Released: 2014-04-09 
• Deposition Author(s): Tan, K., Gu, M., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 
  0.149 (Depositor), 0.150 (DCC) 
• R-Value Work: 
  0.128 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.129 (Depositor) 

Literature

The crystal structure of a solute binding protein from Bacillus anthracis str. Ames in complex with quorum-sensing signal autoinducer-2 (AI-2).

Tan, K., Gu, M., Kwon, K., Anderson, W.F., Joachimiak, A.

To be published.

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: 36.64 kDa 
• Atom Count: 2,884 
• Modeled Residue Count: 321 
• Deposited Residue Count: 324 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
sugar ABC transporter, sugar-binding protein	A	324	Bacillus anthracis str. Ames	Mutation(s): 0  Gene Names: BA_2975, BAS2763, GBAA_2975
UniProt
Find proteins for A0A6H3AKG3 (Bacillus anthracis) Explore A0A6H3AKG3  Go to UniProtKB:  A0A6H3AKG3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PAV	B [auth A]	(2R,4S)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran C5 H10 O5 BVIYGXUQVXBHQS-IUYQGCFVSA-N
EDO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	J [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.149 (Depositor), 0.150 (DCC) 
• R-Value Work:  0.128 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.129 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34pz0

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.005	α = 90
b = 58.067	β = 95.58
c = 63.194	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-09 
Deposition Author(s): Tan, K., Gu, M., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2014-04-09
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Database references, Derived calculations, Structure summary
• Version 2.1: 2024-11-27
  Changes: Data collection, Database references, Structure summary