› 2vvd

X-ray diffraction
2.26Å resolution

Crystal structure of the receptor binding domain of the spike protein P1 from bacteriophage PM2

Released:
DOI: 10.2210/pdb2vvd/pdb
Model geometry
Fit model/data
PDB entry 2vvd coloured by chain, front view.
PDB entry 2vvd coloured by chain, side view.
PDB entry 2vvd coloured by chain, top view.
Source organism: Pseudoalteromonas virus PM2
Primary publication:
Insights into virus evolution and membrane biogenesis from the structure of the marine lipid-containing bacteriophage PM2.
Abrescia NG, Grimes JM, Kivelä HM, Assenberg R, Sutton GC, Butcher SJ, Bamford JK, Bamford DH, Stuart DI
Mol Cell 31 749-61 (2008)
PMID: 18775333

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-195031 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Spike protein P1 Chain: A
Molecule details ›
Chain: A
Length: 177 amino acids
Theoretical weight: 20.17 KDa
Source organism: Pseudoalteromonas virus PM2
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9XJR3 (Residues: 159-335; Coverage: 53%)
Gene name: I
Sequence domains: Phage PM2 spike protein P1
Structure domains: Jelly Rolls

Ligands and Environments

1 bound ligand:
Ligand CA 2 x CA
1 modified residue:
Ligand MSE 2 x MSE

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: ESRF BEAMLINE BM14
Spacegroup: P212121
Unit cell:
a: 43.645Å b: 49.055Å c: 72.177Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.172 0.169 0.228
Expression system: Escherichia coli

Quick links

Citations

23 review citations

Phage diversity, genomics and phylogeny.
Dion et al. (2020)
22 more

1 mention without citation

From lows to highs: using low-resolution models to phase X-ray data.
Stuart et al. (2013)

PDB-REDO

The sliders below show the change in model quality between original PDB entry and the PDB-REDO entry

Model Geometry
 
 
Data not available
DNA/RNA Geometry
 
 
Data not available
Fit model/data
 
 
Data not available
PDB-REDO