› 4ns1

X-ray diffraction
1.64Å resolution

Crystal structure of purine nucleoside phosphorylase from Porphyromonas gingivalis ATCC 33277, NYSGRC Target 30972

Released:
DOI: 10.2210/pdb4ns1/pdb
PDB entry 4ns1 coloured by chain, front view.
PDB entry 4ns1 coloured by chain, side view.
PDB entry 4ns1 coloured by chain, top view.
Source organism: Porphyromonas gingivalis ATCC 33277
Entry authors: Malashkevich VN, Bhosle R, Toro R, Hillerich B, Gizzi A, Garforth S, Kar A, Chan MK, Lafluer J, Patel H, Matikainen B, Chamala S, Lim S, Celikgil A, Villegas G, Evans B, Love J, Fiser A, Seidel R, Bonanno JB, Almo SC, New York Structural Genomics Research Consortium (NYSGRC)

Function and Biology Details

Reaction catalysed: 
Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-109709 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Purine nucleoside phosphorylase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 295 amino acids
Theoretical weight: 32.79 KDa
Source organism: Porphyromonas gingivalis ATCC 33277
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: B2RKN6 (Residues: 1-273; Coverage: 100%)
Gene name: PGN_1412
Sequence domains: Phosphorylase superfamily
Structure domains: Nucleoside phosphorylase domain

Ligands and Environments

3 bound ligands:
Ligand D5M 4 x D5M
Ligand SO4 7 x SO4
Ligand GOL 11 x GOL
2 modified residues:
Ligand MSE 48 x MSE
Ligand CSO 4 x CSO

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: I213
Unit cell:
a: 218.904Å b: 218.904Å c: 218.904Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.172 0.171 0.186
Expression system: Escherichia coli BL21(DE3)

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