› 4pcd

X-ray diffraction
1.7Å resolution

CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM ROSEOBACTER DENITRIFICANS OCh 114 (RD1_1052, TARGET EFI-510238) WITH BOUND L-GALACTONATE

Released:
DOI: 10.2210/pdb4pcd/pdb
PDB entry 4pcd coloured by chain, front view.
PDB entry 4pcd coloured by chain, side view.
PDB entry 4pcd coloured by chain, top view.
Source organism: Roseobacter denitrificans OCh 114
Primary publication:
Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes.
Vetting MW, Al-Obaidi N, Zhao S, San Francisco B, Kim J, Wichelecki DJ, Bouvier JT, Solbiati JO, Vu H, Zhang X, Rodionov DA, Love JD, Hillerich BS, Seidel RD, Quinn RJ, Osterman AL, Cronan JE, Jacobson MP, Gerlt JA, Almo SC
Biochemistry 54 909-31 (2015)
PMID: 25540822

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-172620 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Solute-binding protein RD1_1052 Chain: A
Molecule details ›
Chain: A
Length: 322 amino acids
Theoretical weight: 36.07 KDa
Source organism: Roseobacter denitrificans OCh 114
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q16BC9 (Residues: 27-325; Coverage: 100%)
Gene name: RD1_1052
Sequence domains: Bacterial extracellular solute-binding protein, family 7
Structure domains: Bacterial extracellular solute-binding protein, family 7

Ligands and Environments

1 bound ligand:
Ligand 2Q2 1 x 2Q2
1 modified residue:
Ligand MSE 12 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 31-ID
Spacegroup: P212121
Unit cell:
a: 52.375Å b: 73.26Å c: 75.889Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.138 0.135 0.179
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

13 review citations

Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks.
Gerlt et al. (2015)
12 more

1 mention without citation

Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes.
Vetting et al. (2015)