› 7mpq

X-ray diffraction
2.35Å resolution

Bartonella henselae NrnC cleaving pGG in the presence of Mn2+

Released:
DOI: 10.2210/pdb7mpq/pdb
PDB entry 7mpq coloured by chain, front view.
PDB entry 7mpq coloured by chain, side view.
PDB entry 7mpq coloured by chain, top view.
Source organisms:
Primary publication:
Structural characterization of NrnC identifies unifying features of dinucleotidases.
Lormand JD, Kim SK, Walters-Marrah GA, Brownfield BA, Fromme JC, Winkler WC, Goodson JR, Lee VT, Sondermann H
Elife 10 (2021)
PMID: 34533457

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero nonamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-197289 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
3'-5' exonuclease Chains: A, C, E, G, I, K, M, O
Molecule details ›
Chains: A, C, E, G, I, K, M, O
Length: 207 amino acids
Theoretical weight: 23.45 KDa
Source organism: Bartonella henselae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: X5MEI1 (Residues: 1-206; Coverage: 100%)
Gene name: BM1374165_00260
Sequence domains: 3'-5' exonuclease
5'-phosphorylated GG Chain: R
Molecule details ›
Chain: R
Length: 2 nucleotides
Theoretical weight: 645 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand 5GP 14 x 5GP
Ligand MN 16 x MN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P21
Unit cell:
a: 71.681Å b: 127.799Å c: 128.809Å
α: 90° β: 94.872° γ: 90°
R-values:
R R work R free
0.164 0.162 0.206
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

2 review citations

Nano-RNases: oligo- or dinucleases?
Lee et al. (2022)
1 more

1 mention without citation

Structural characterization of NrnC identifies unifying features of dinucleotidases.
Lormand et al. (2021)