› 4mar

X-ray diffraction
2.16Å resolution

Crystal structure of purine nucleoside phosphorylase from Meiothermus ruber DSM 1279 complexed with sulfate.

Released:
DOI: 10.2210/pdb4mar/pdb
PDB entry 4mar coloured by chain, front view.
PDB entry 4mar coloured by chain, side view.
PDB entry 4mar coloured by chain, top view.
Source organism: Meiothermus ruber DSM 1279
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, Khafizov K, Seidel R, Bonanno JB, Almo SC, New York Structural Genomics Research Consortium (NYSGRC)

Function and Biology Details

Reaction catalysed: 
Uridine + phosphate = uracil + alpha-D-ribose 1-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-112532 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Uridine phosphorylase Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 254 amino acids
Theoretical weight: 28.41 KDa
Source organism: Meiothermus ruber DSM 1279
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: D3PPS9 (Residues: 1-232; Coverage: 100%)
Gene names: K649_07785, Mrub_2947, deoD
Sequence domains: Phosphorylase superfamily
Structure domains: Nucleoside phosphorylase domain

Ligands and Environments

2 bound ligands:
Ligand MG 1 x MG
Ligand SO4 11 x SO4
1 modified residue:
Ligand MSE 21 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 31-ID
Spacegroup: C2221
Unit cell:
a: 57.403Å b: 189.103Å c: 152.235Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.19 0.188 0.226
Expression system: Escherichia coli BL21(DE3)

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