2FW0 | pdb_00002fw0

Apo Open Form of Glucose/Galactose Binding Protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 
    0.178 (Depositor), 0.180 (DCC) 
  • R-Value Work: 
    0.165 (Depositor), 0.167 (DCC) 
  • R-Value Observed: 
    0.165 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2FW0

This is version 1.4 of the entry. See complete history

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

  • DOI: https://doi.org/10.1110/ps.062707807
  • Primary Citation 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.


  • Organizational Affiliation
    • Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA.

Macromolecule Content 

  • Total Structure Weight: 33.81 kDa 
  • Atom Count: 2,706 
  • Modeled Residue Count: 305 
  • Deposited Residue Count: 309 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
D-galactose-binding periplasmic protein309Escherichia coliMutation(s): 0 
Gene Names: mglB
UniProt
Find proteins for P0AEE5 (Escherichia coli (strain K12))
Explore P0AEE5 
Go to UniProtKB:  P0AEE5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AEE5
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CIT

Query on CIT



Download:Ideal Coordinates CCD File
F [auth A]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
MLA

Query on MLA



Download:Ideal Coordinates CCD File
G [auth A]MALONIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
E [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free:  0.178 (Depositor), 0.180 (DCC) 
  • R-Value Work:  0.165 (Depositor), 0.167 (DCC) 
  • R-Value Observed: 0.165 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.8α = 90
b = 70.3β = 90
c = 112.1γ = 90
Software Package:
Software NamePurpose
CNSrefinement
SAINTdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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: Version format compliance
  • Version 1.3: 2015-04-29
    Changes: Non-polymer description
  • Version 1.4: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description