› 5trd

X-ray diffraction
1.85Å resolution

Structure of RbkR (Riboflavin Kinase) from Thermoplasma acidophilum determined in complex with CTP and its cognate DNA operator

Released:
DOI: 10.2210/pdb5trd/pdb
PDB entry 5trd coloured by chain, front view.
PDB entry 5trd coloured by chain, side view.
PDB entry 5trd coloured by chain, top view.
Source organisms:
Entry authors: Vetting MW, Rodionova IA, Li X, Osterman AL, Rodionov DA, Almo SC

Function and Biology Details

Reaction catalysed: 
CTP + riboflavin = CDP + FMN
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119155 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Riboflavin kinase Chains: A, B
Molecule details ›
Chains: A, B
Length: 230 amino acids
Theoretical weight: 26.25 KDa
Source organism: Thermoplasma acidophilum DSM 1728
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9HJA6 (Residues: 2-220; Coverage: 100%)
Gene names: Ta1064, ribK
Sequence domains:
Structure domains:
DNA (5'-D(*AP*TP*TP*AP*CP*TP*AP*AP*TP*TP*CP*AP*CP*GP*AP*GP*TP*AP*A)-3') Chain: G
Molecule details ›
Chain: G
Length: 19 nucleotides
Theoretical weight: 5.81 KDa
Source organism: Thermoplasma acidophilum
Expression system: Not provided
DNA (5'-D(P*TP*TP*TP*AP*CP*TP*CP*GP*TP*GP*AP*AP*TP*TP*AP*GP*TP*AP*A)-3') Chain: H
Molecule details ›
Chain: H
Length: 19 nucleotides
Theoretical weight: 5.83 KDa
Source organism: Thermoplasma acidophilum
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand CTP 2 x CTP
Ligand NA 2 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 31-ID
Spacegroup: P21
Unit cell:
a: 58.411Å b: 95.04Å c: 61.262Å
α: 90° β: 113.51° γ: 90°
R-values:
R R work R free
0.176 0.174 0.216
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

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