› 4m1e

X-ray diffraction
1.9Å resolution

Crystal structure of purine nucleoside phosphorylase I from Planctomyces limnophilus DSM 3776, NYSGRC Target 029364.

Released:
DOI: 10.2210/pdb4m1e/pdb
PDB entry 4m1e coloured by chain, front view.
PDB entry 4m1e coloured by chain, side view.
PDB entry 4m1e coloured by chain, top view.
Source organism: Planctopirus limnophila DSM 3776
Entry authors: Malashkevich VN, Bonanno JB, 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, Khafizov K, Seidel R, 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

Assemblies composition:
homo trimer (preferred)
homo hexamer
Assembly name:
PDBe Complex ID:
PDB-CPX-112726 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Purine nucleoside phosphorylase Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 297 amino acids
Theoretical weight: 32.99 KDa
Source organism: Planctopirus limnophila DSM 3776
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: D5SMY7 (Residues: 1-275; Coverage: 100%)
Gene name: Plim_2216
Sequence domains: Phosphorylase superfamily
Structure domains: Nucleoside phosphorylase domain

Ligands and Environments

3 bound ligands:
Ligand SO4 6 x SO4
Ligand ADE 6 x ADE
Ligand 6PC 6 x 6PC
1 modified residue:
Ligand MSE 72 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 31-ID
Spacegroup: P1
Unit cell:
a: 80.95Å b: 81.06Å c: 91.616Å
α: 103.42° β: 105.36° γ: 112.73°
R-values:
R R work R free
0.215 0.213 0.258
Expression system: Escherichia coli BL21(DE3)

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