› 8ka0

X-ray diffraction
2.35Å resolution

Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) complexed with Ca2+-bound calmodulin and a nicotinamide adenine dinucleotide (NAD+)

Released:
DOI: 10.2210/pdb8ka0/pdb
PDB entry 8ka0 coloured by chain, front view.
PDB entry 8ka0 coloured by chain, side view.
PDB entry 8ka0 coloured by chain, top view.
Source organisms:
Primary publication:
Dissemination of pathogenic bacteria is reinforced by a MARTX toxin effector duet.
Choi S, Lee Y, Park S, Jang SY, Park J, Oh DW, Kim SM, Kim TH, Lee GS, Cho C, Kim BS, Lee D, Kim EH, Cheong HK, Moon JH, Song JJ, Hwang J, Kim MH
Nat Commun 15 6218 (2024)
PMID: 39043696

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-246745 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
N-epsilon-fatty acyltransferase F2 Chains: A, C, E, G
Molecule details ›
Chains: A, C, E, G
Length: 416 amino acids
Theoretical weight: 47.09 KDa
Source organism: Vibrio vulnificus
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A2S3R7M0 (Residues: 1959-2374; Coverage: 8%)
Gene name: CRN52_02910
Calmodulin-2 Chains: B, D, F, H
Molecule details ›
Chains: B, D, F, H
Length: 151 amino acids
Theoretical weight: 16.98 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0DP24 (Residues: 1-149; Coverage: 100%)
Gene names: CALM2, CAM2, CAMB
Sequence domains: EF-hand domain pair

Ligands and Environments

3 bound ligands:
Ligand NAD 4 x NAD
Ligand CA 8 x CA
Ligand GOL 4 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PAL/PLS BEAMLINE 5C (4A)
Spacegroup: P21
Unit cell:
a: 136.222Å b: 48.931Å c: 178.603Å
α: 90° β: 95.7° γ: 90°
R-values:
R R work R free
0.22 0.217 0.263
Expression system: Escherichia coli

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