› 3mbj

X-ray diffraction
2.1Å resolution

Crystal structure of a putative phosphomethylpyrimidine kinase (BT_4458) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.10 A resolution (rhombohedral form)

Released:
DOI: 10.2210/pdb3mbj/pdb
PDB entry 3mbj coloured by chain, front view.
PDB entry 3mbj coloured by chain, side view.
PDB entry 3mbj coloured by chain, top view.
Source organism: Bacteroides thetaiotaomicron VPI-5482
Entry author: Joint Center for Structural Genomics (JCSG)

Function and Biology Details

Reaction catalysed: 
ATP + pyridoxal = ADP + pyridoxal 5'-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-183577 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
pyridoxal kinase Chain: A
Molecule details ›
Chain: A
Length: 291 amino acids
Theoretical weight: 33.43 KDa
Source organism: Bacteroides thetaiotaomicron VPI-5482
Expression system: Escherichia coli
UniProt:
  • Canonical: Q89ZB9 (Residues: 1-290; Coverage: 100%)
Gene name: BT_4458
Sequence domains: Phosphomethylpyrimidine kinase
Structure domains: UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase

Ligands and Environments

6 bound ligands:
Ligand ZN 3 x ZN
Ligand CL 1 x CL
Ligand SO4 2 x SO4
Ligand IMD 1 x IMD
Ligand MPD 2 x MPD
Ligand MRD 2 x MRD
1 modified residue:
Ligand MSE 11 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL11-1
Spacegroup: R32
Unit cell:
a: 161.627Å b: 161.627Å c: 76.138Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.173 0.171 0.21
Expression system: Escherichia coli

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