PDBe 5im4

X-ray diffraction
3.5Å resolution

Crystal structure of designed two-component self-assembling icosahedral cage I52-32

Released:

Function and Biology Details

Reaction catalysed:
1-deoxy-L-glycero-tetrulose 4-phosphate + 5-amino-6-(D-ribitylamino)uracil = 6,7-dimethyl-8-(D-ribityl)lumazine + 2 H(2)O + phosphate
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero 120-mer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
6,7-dimethyl-8-ribityllumazine synthase Chains: A, B, C, D, E, K, L, M, N, O, U, V, W, X, Y, e, f, g, h, i
Molecule details ›
Chains: A, B, C, D, E, K, L, M, N, O, U, V, W, X, Y, e, f, g, h, i
Length: 162 amino acids
Theoretical weight: 18.1 KDa
Source organism: Candida albicans P37005
Expression system: Escherichia coli BL21(DE3)
Structure domains: Lumazine/riboflavin synthase
Phosphotransferase system, mannose/fructose-specific component IIA Chains: F, G, H, I, J, P, Q, R, S, T, Z, a, b, c, d, j, k, l, m, n
Molecule details ›
Chains: F, G, H, I, J, P, Q, R, S, T, Z, a, b, c, d, j, k, l, m, n
Length: 138 amino acids
Theoretical weight: 15.16 KDa
Source organism: Caldanaerobacter subterraneus subsp. tengcongensis MB4
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8RD55 (Residues: 1-136; Coverage: 100%)
Gene names: ManX, TTE0192
Sequence domains: PTS system fructose IIA component
Structure domains: Phosphotransferase system, mannose-type IIA component

Ligands and Environments

No bound ligands

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: R3
Unit cell:
a: 258.82Å b: 258.82Å c: 641.73Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.228 0.227 0.233
Expression system: Escherichia coli BL21(DE3)