Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 33.82 kDa 
• Atom Count: 2837 
• Modelled Residue Count: 305 
• Deposited Residue Count: 309 
• Unique protein chains: 1

2FVY

High Resolution Glucose Bound Crystal Structure of GGBP

• DOI: 10.2210/pdb2FVY/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-01-31 Released: 2007-02-06 
• Deposition Author(s): Borrok, M.J., Kiessling, L.L., Forest, K.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.92 Å
• R-Value Free: 0.130 
• R-Value Work: 0.110 
• R-Value Observed: 0.118 

Literature

Conformational changes of glucose/galactose-binding protein illuminated by open, unliganded, and ultra-high-resolution ligand-bound structures.

Borrok, M.J., Kiessling, L.L., Forest, K.T.

(2007) Protein Sci 16: 1032-1041

• PubMed: 17473016 
• DOI: 10.1110/ps.062707807
• Primary Citation of Related Structures:  
  2FVY, 2FW0


• PubMed Abstract: 
  

D-Glucose/D-Galactose-binding protein (GGBP) mediates chemotaxis toward and active transport of glucose and galactose in a number of bacterial species. GGBP, like other periplasmic binding proteins, can exist in open (ligand-free) and closed (ligand-bound) states. We report a 0.92 angstroms resolution structure of GGBP from Escherichia coli in the glucose-bound state and the first structure of an open, unbound form of GGBP (at 1.55 angstroms resolution). These structures vary in the angle between the two structural domains; the observed difference of 31 degrees arises from torsion angle changes in a three-segment hinge. A comparison with the closely related periplasmic receptors, ribose- and allose-binding proteins, shows that the GGBP hinge residue positions that undergo the largest conformational changes are different. Furthermore, the high-quality data collected for the atomic resolution glucose-bound structure allow for the refinement of specific hydrogen atom positions, the assignment of alternate side chain conformations, the first description of CO(2) trapped after radiation-induced decarboxylation, and insight into the role of the exo-anomeric effect in sugar binding. Together, these structures provide insight into how the hinge-bending movement of GGBP facilitates ligand binding, transport, and signaling.

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Organizational Affiliation: 

Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-galactose-binding periplasmic protein	A	309	Escherichia coli	Mutation(s): 0  Gene Names: mglB
Find proteins for P0AEE5 (Escherichia coli (strain K12)) Explore P0AEE5  Go to UniProtKB:  P0AEE5

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BGC	B [auth A]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CO2	E [auth A]	CARBON DIOXIDE C O2 CURLTUGMZLYLDI-UHFFFAOYSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.92 Å
• R-Value Free: 0.130 
• R-Value Work: 0.110 
• R-Value Observed: 0.118 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.989	α = 90
b = 36.238	β = 124.5
c = 80.101	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-01-31 
• Released Date: 2007-02-06 
Deposition Author(s): Borrok, M.J., Kiessling, L.L., Forest, K.T.

Revision History  

• Version 1.0: 2007-02-06
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Version format compliance
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2020-09-02
  Changes: Structure summary
• Version 2.2: 2020-10-21
  Changes: Derived calculations