› 3kdr

X-ray diffraction
2.9Å resolution

The Crystal Structure of a HK97 Family Phage Portal Protein from Corynebacterium diphtheriae to 2.9A

Released:
DOI: 10.2210/pdb3kdr/pdb
PDB entry 3kdr coloured by chain, front view.
PDB entry 3kdr coloured by chain, side view.
PDB entry 3kdr coloured by chain, top view.
Source organism: Corynebacterium diphtheriae
Entry authors: Nocek B, Stein AJ, Mulligan R, Duggan E, Abdullah J, Joachimiak A, Midwest Center for Structural Genomics (MCSG)

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
homo dodecamer (preferred)
homo 72-mer
Assembly name:
PDBe Complex ID:
PDB-CPX-180036 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Phage portal protein Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 310 amino acids
Theoretical weight: 33.27 KDa
Source organism: Corynebacterium diphtheriae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q6NFR1 (Residues: 40-349; Coverage: 89%)
Gene name: DIP1825
Sequence domains: Phage portal protein
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand PO4 2 x PO4
Ligand GOL 2 x GOL
Ligand SO4 2 x SO4
1 modified residue:
Ligand MSE 24 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: F432
Unit cell:
a: 340.068Å b: 340.068Å c: 340.068Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.2 0.198 0.245
Expression system: Escherichia coli BL21(DE3)

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