› 4rs3

X-ray diffraction
1.4Å resolution

Crystal structure of carbohydrate transporter A0QYB3 from Mycobacterium smegmatis str. MC2 155, target EFI-510969, in complex with xylitol

Released:
DOI: 10.2210/pdb4rs3/pdb
PDB entry 4rs3 coloured by chain, front view.
PDB entry 4rs3 coloured by chain, side view.
PDB entry 4rs3 coloured by chain, top view.
Source organism: Mycolicibacterium smegmatis MC2 155
Primary publication:
A General Strategy for the Discovery of Metabolic Pathways: d-Threitol, l-Threitol, and Erythritol Utilization in Mycobacterium smegmatis.
Huang H, Carter MS, Vetting MW, Al-Obaidi N, Patskovsky Y, Almo SC, Gerlt JA
J Am Chem Soc 137 14570-3 (2015)
PMID: 26560079

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-106375 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Xylitol-binding protein Chain: A
Molecule details ›
Chain: A
Length: 327 amino acids
Theoretical weight: 34.61 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0QYB3 (Residues: 25-349; Coverage: 99%)
Gene names: MSMEG_3598, MSMEI_3515, xypA
Sequence domains: Periplasmic binding protein domain
Structure domains: Rossmann fold

Ligands and Environments

5 bound ligands:
Ligand XYL 1 x XYL
Ligand ZN 11 x ZN
Ligand IMD 4 x IMD
Ligand CL 16 x CL
Ligand ACT 4 x ACT
1 modified residue:
Ligand MSE 9 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 31-ID
Spacegroup: P212121
Unit cell:
a: 62.841Å b: 63.07Å c: 73.134Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.125 0.124 0.163
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

5 review citations

Synthetic metabolism: metabolic engineering meets enzyme design.
Erb et al. (2017)
4 more

1 mention without citation

Structural Flexibility of Peripheral Loops and Extended C-terminal Domain of Short Length Substrate Binding Protein from Rhodothermus marinus.
Bae et al. (2021)