PDBsum entry 2gh7

Biotin binding protein

PDB id: 2gh7

Contents

Protein chains

121 a.a. *

Ligands

BTN-BTQ ×2

GOL ×3

Waters ×273

* Residue conservation analysis

PDB id:

2gh7

Name:

Biotin binding protein

Title:

Epi-biotin complex with core streptavidin

Structure:

Streptavidin. Chain: a, b. Engineered: yes

Source:

Streptomyces avidinii. Organism_taxid: 1895. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Tetramer (from PDB file)

Resolution:

1.00Å R-factor: 0.144 R-free: 0.152

Authors:

I.Le Trong,D.G.L.Aubert,N.R.Thomas,R.E.Stenkamp

Key ref:

I.Le Trong et al. (2006). The high-resolution structure of (+)-epi-biotin bound to streptavidin. Acta Crystallogr D Biol Crystallogr, 62, 576-581. PubMed id: 16699183 DOI: 10.1107/S0907444906011887

Date:

26-Mar-06 Release date: 18-Apr-06

Protein chains

P22629  (SAV_STRAV) -  Streptavidin from Streptomyces avidinii

Seq: 183 a.a.

Struc: 121 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1107/S0907444906011887

Acta Crystallogr D Biol Crystallogr 62:576-581 (2006)

PubMed id: 16699183

The high-resolution structure of (+)-epi-biotin bound to streptavidin.

I.Le Trong, D.G.Aubert, N.R.Thomas, R.E.Stenkamp.

ABSTRACT

(+)-Epi-biotin differs from (+)-biotin in the configuration of the chiral center at atom C2. This could lead to a difference in the mode of binding of (+)-epi-biotin to streptavidin, a natural protein receptor for (+)-biotin. Diffraction data were collected to a maximum of 0.85 Angstrom resolution for structural analysis of the complex of streptavidin with a sample of (+)-epi-biotin and refinement was carried out at both 1.0 and 0.85 Angstrom resolution. The structure determination shows a superposition of two ligands in the binding site, (+)-biotin and (+)-epi-biotin. The molecules overlap in the model for the complex except for the position of S1 in the tetrahydrothiophene ring. Differences in the conformation of the ring permits binding of each molecule to streptavidin with little observable difference in the protein structures at this high resolution.

Selected figure(s)

Figure 2.
Figure 2 (a) Difference electron density for one binding site after refinement including the biotin molecule in the model. (b) Difference electron density after making the thermal parameter of the S atom consistent with those of the neighboring atoms. Negative densities are shown in red (-4 ) and positive in blue (4 ) and cyan (5 ).

Figure 5.
Figure 5 Difference electron-density map showing the positive peaks associated with H atoms on a -strand at the center of the molecule. Positive contours are shown at 3 (blue), 4 (purple) and 5 (cyan); negative contours are shown at -3 (red). The |F[o]| - |F[c]| map was calculated using phases and |F[c]| for the model just prior to the addition of H atoms at their calculated positions.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2006, 62, 576-581) copyright 2006.

Figures were selected by the author.

Author's comment

Figure 2 shows the experimental evidence (difference density) for the ligand being a mix of two enantiomers.
Figure 5 shows that we can see hydrogen atoms.
Ron Stenkamp