› 6dt3

X-ray diffraction
1.2Å resolution

1.2 Angstrom Resolution Crystal Structure of Nucleoside Triphosphatase NudI from Klebsiella pneumoniae in Complex with HEPES

Released:
DOI: 10.2210/pdb6dt3/pdb
PDB entry 6dt3 coloured by chain, front view.
PDB entry 6dt3 coloured by chain, side view.
PDB entry 6dt3 coloured by chain, top view.
Source organism: Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044
Primary publication:
A Structural Systems Biology Approach to High-Risk CG23 Klebsiella pneumoniae.
Inniss NL, Kochan TJ, Minasov G, Wawrzak Z, Chang C, Tan K, Shuvalova L, Kiryukhina O, Pshenychnyi S, Wu R, Dubrovska I, Babnigg G, Endres M, Anderson WF, Hauser AR, Joachimiak A, Satchell KJF
Microbiol Resour Announc 12 e0101322 (2023)
PMID: 36695589

Function and Biology Details

Reactions catalysed: 
dCTP + H(2)O = dCMP + diphosphate
dUTP + H(2)O = dUMP + diphosphate
A nucleoside triphosphate + H(2)O = a nucleotide + diphosphate
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-103827 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nucleoside triphosphatase NudI Chains: A, B
Molecule details ›
Chains: A, B
Length: 144 amino acids
Theoretical weight: 16.65 KDa
Source organism: Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A1W1Q5B1 (Residues: 1-141; Coverage: 100%)
Gene names: NCTC11679_01637, SAMEA3512100_01068, nudI
Sequence domains: NUDIX domain
Structure domains: Nucleoside Triphosphate Pyrophosphohydrolase

Ligands and Environments

1 bound ligand:
Ligand EPE 1 x EPE
1 modified residue:
Ligand MSE 6 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: P1
Unit cell:
a: 33.14Å b: 39.346Å c: 56.294Å
α: 77.07° β: 80.74° γ: 86.2°
R-values:
R R work R free
0.155 0.153 0.187
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 citations in other articles

Klebsiella pneumoniae clinical isolates with features of both multidrug-resistance and hypervirulence have unexpectedly low virulence.
Kochan et al. (2023)

1 mention without citation

A Structural Systems Biology Approach to High-Risk CG23 Klebsiella pneumoniae.
Inniss et al. (2023)