› 3m1u

X-ray diffraction
1.75Å resolution

Crystal structure of a Putative gamma-D-glutamyl-L-diamino acid endopeptidase (DVU_0896) from DESULFOVIBRIO VULGARIS HILDENBOROUGH at 1.75 A resolution

Released:
DOI: 10.2210/pdb3m1u/pdb
PDB entry 3m1u coloured by chain, front view.
PDB entry 3m1u coloured by chain, side view.
PDB entry 3m1u coloured by chain, top view.
Source organism: Desulfovibrio vulgaris str. Hildenborough
Entry author: Joint Center for Structural Genomics (JCSG)

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-180794 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Lipoprotein, NLP/P60 family Chains: A, B
Molecule details ›
Chains: A, B
Length: 434 amino acids
Theoretical weight: 47.75 KDa
Source organism: Desulfovibrio vulgaris str. Hildenborough
Expression system: Escherichia coli
UniProt:
  • Canonical: Q72DN3 (Residues: 32-464; Coverage: 99%)
Gene name: DVU_0896
Sequence domains:
Structure domains: endopeptidase domain like (from Nostoc punctiforme)

Ligands and Environments

4 bound ligands:
Ligand GOL 11 x GOL
Ligand ACT 2 x ACT
Ligand MES 2 x MES
Ligand CL 9 x CL
1 modified residue:
Ligand MSE 30 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-2
Spacegroup: P21
Unit cell:
a: 59.337Å b: 54.465Å c: 122.982Å
α: 90° β: 94.06° γ: 90°
R-values:
R R work R free
0.141 0.139 0.173
Expression system: Escherichia coli

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