PDBe 5im5

X-ray diffraction
3.7Å resolution

Crystal structure of designed two-component self-assembling icosahedral cage I53-40

Released:

Function and Biology Details

Reaction catalysed:
2 6,7-dimethyl-8-(1-D-ribityl)lumazine = riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero 120-mer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Riboflavin synthase Chains: A, B, C, D, E, F, G, H, I, J, K, M, O, Q, S
Molecule details ›
Chains: A, B, C, D, E, F, G, H, I, J, K, M, O, Q, S
Length: 156 amino acids
Theoretical weight: 17.25 KDa
Source organism: Methanocaldococcus jannaschii DSM 2661
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q58584 (Residues: 1-156; Coverage: 100%)
Gene names: MJ1184, ribC
Sequence domains: 6,7-dimethyl-8-ribityllumazine synthase
Structure domains: Lumazine/riboflavin synthase
Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase Chains: 1, 2, 3, 4, L, N, P, R, T, U, V, W, X, Y, Z
Molecule details ›
Chains: 1, 2, 3, 4, L, N, P, R, T, U, V, W, X, Y, Z
Length: 219 amino acids
Theoretical weight: 23.15 KDa
Source organism: Vibrionales bacterium SWAT-3
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A5KUH7 (Residues: 1-209; Coverage: 100%)
Gene name: VSWAT3_13722
Sequence domains: KDPG and KHG aldolase
Structure domains: Aldolase class I

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: I222
Unit cell:
a: 265.62Å b: 279.81Å c: 301.33Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.241 0.24 0.247
Expression system: Escherichia coli BL21(DE3)