› 3nyy

X-ray diffraction
1.6Å resolution

Crystal structure of a putative glycyl-glycine endopeptidase lytM (RUMGNA_02482) from Ruminococcus gnavus ATCC 29149 at 1.60 A resolution

Released:
DOI: 10.2210/pdb3nyy/pdb
PDB entry 3nyy coloured by chain, front view.
PDB entry 3nyy coloured by chain, side view.
PDB entry 3nyy coloured by chain, top view.
Source organism: [Ruminococcus] gnavus ATCC 29149
Entry author: Joint Center for Structural Genomics (JCSG)

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-108233 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Peptidase, M23 family Chain: A
Molecule details ›
Chain: A
Length: 252 amino acids
Theoretical weight: 28.98 KDa
Source organism: [Ruminococcus] gnavus ATCC 29149
Expression system: Escherichia coli
UniProt:
  • Canonical: A7B4J8 (Residues: 29-279; Coverage: 90%)
Gene name: RUMGNA_02482
Sequence domains:

Ligands and Environments

2 bound ligands:
Ligand 2PE 3 x 2PE
Ligand SO4 4 x SO4
1 modified residue:
Ligand MSE 6 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL11-1
Spacegroup: C2
Unit cell:
a: 91.336Å b: 61.572Å c: 52.804Å
α: 90° β: 108.5° γ: 90°
R-values:
R R work R free
0.15 0.149 0.175
Expression system: Escherichia coli

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