› 6k4r

X-ray diffraction
3.11Å resolution

Crystal structure of SidJ-CaM-AMP ternary complex at 3.11 A

Released:
DOI: 10.2210/pdb6k4r/pdb
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PDB entry 6k4r coloured by chain, front view.
PDB entry 6k4r coloured by chain, side view.
PDB entry 6k4r coloured by chain, top view.
Source organisms:
Primary publication:
Regulation of phosphoribosyl ubiquitination by a calmodulin-dependent glutamylase.
Gan N, Zhen X, Liu Y, Xu X, He C, Qiu J, Liu Y, Fujimoto GM, Nakayasu ES, Zhou B, Zhao L, Puvar K, Das C, Ouyang S, Luo ZQ
OpenAccess logo Nature 572 387-391 (2019)
PMID: 31330531

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-143952 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Calmodulin-dependent glutamylase SidJ Chains: A, B
Molecule details ›
Chains: A, B
Length: 873 amino acids
Theoretical weight: 100.34 KDa
Source organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q5ZTK6 (Residues: 1-873; Coverage: 100%)
Gene names: lpg2155, sidJ
Calmodulin-1 Chains: C, D
Molecule details ›
Chains: C, D
Length: 149 amino acids
Theoretical weight: 16.85 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0DP23 (Residues: 1-149; Coverage: 100%)
Gene names: CALM, CALM1, CAM, CAM1
Sequence domains: EF-hand domain pair

Ligands and Environments

4 bound ligands:
Ligand AMP 2 x AMP
Ligand CL 4 x CL
Ligand PG4 2 x PG4
Ligand CA 2 x CA
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: P21
Unit cell:
a: 60.846Å b: 159.178Å c: 135.032Å
α: 90° β: 101.78° γ: 90°
R-values:
R R work R free
0.241 0.239 0.279
Expression systems:
  • Escherichia coli BL21(DE3)
  • Escherichia coli

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Citations

17 review citations

Tutorial: best practices and considerations for mass-spectrometry-based protein biomarker discovery and validation.
Nakayasu et al. (2021)
16 more

3 mentions without citation

Catalytic activity regulation through post-translational modification: the expanding universe of protein diversity.
Kokkinidis et al. (2020)
2 more

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