› 5fcd

X-ray diffraction
2.1Å resolution

Crystal structure of MccD protein

Released:
DOI: 10.2210/pdb5fcd/pdb
PDB entry 5fcd coloured by chain, front view.
PDB entry 5fcd coloured by chain, side view.
PDB entry 5fcd coloured by chain, top view.
Source organism: Escherichia coli
Entry authors: Nocek B, Jedrzejczak R, Anderson WF, Severinov K, Dubiley S, Joachimiak A, Center for Structural Genomics of Infectious Diseases (CSGID)

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero dimer
hetero dodecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-165649 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
UNK-UNK-UNK-MSE-UNK Chain: D
Molecule details ›
Chain: D
Length: 5 amino acids
Theoretical weight: 537 Da
Source organism: Escherichia coli
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UNK-UNK-UNK-UNK-MSE-UNK Chain: E
Molecule details ›
Chain: E
Length: 6 amino acids
Theoretical weight: 622 Da
Source organism: Escherichia coli
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
Methyltransferase type 11 domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 267 amino acids
Theoretical weight: 31.6 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: Q83Y56 (Residues: 1-267; Coverage: 100%)
Gene name: mccD
Sequence domains: Methyltransferase domain
Structure domains: Vaccinia Virus protein VP39

Ligands and Environments

1 bound ligand:
Ligand CL 1 x CL
1 modified residue:
Ligand MSE 16 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P63
Unit cell:
a: 95.1Å b: 95.1Å c: 128.685Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.2 0.199 0.223
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'

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