› 3r6d

X-ray diffraction
1.25Å resolution

Crystal structure of NAD-dependent epimerase/dehydratase from Veillonella parvula DSM 2008 with Cz-methylated lysine

Released:
DOI: 10.2210/pdb3r6d/pdb
PDB entry 3r6d coloured by chain, front view.
PDB entry 3r6d coloured by chain, side view.
PDB entry 3r6d coloured by chain, top view.
Source organism: Veillonella parvula DSM 2008
Entry authors: Chang C, Hatzos-Skintges C, Clancy S, Joachimiak A, Midwest Center for Structural Genomics (MCSG)

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-112264 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
NAD(P)-binding domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 221 amino acids
Theoretical weight: 25 KDa
Source organism: Veillonella parvula DSM 2008
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: D1BQI7 (Residues: 2-218; Coverage: 100%)
Gene name: Vpar_0111
Sequence domains: NAD(P)H-binding
Structure domains: NAD(P)-binding Rossmann-like Domain

Ligands and Environments

No bound ligands
2 modified residues:
Ligand MSE 5 x MSE
Ligand MLZ 6 x MLZ

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P212121
Unit cell:
a: 51.446Å b: 60.721Å c: 69.612Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.15 0.148 0.179
Expression system: Escherichia coli BL21(DE3)

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