› 8wzt

X-ray diffraction
1.6Å resolution

SFX structure of an Mn-carbonyl complex immobilized in hen egg white lysozyme microcrystals, 1 microsecond after photoexcitation at RT.

Released:
DOI: 10.2210/pdb8wzt/pdb
PDB entry 8wzt coloured by chain, front view.
PDB entry 8wzt coloured by chain, side view.
PDB entry 8wzt coloured by chain, top view.
Source organism: Gallus gallus
Primary publication:
Real-time observation of a metal complex-driven reaction intermediate using a porous protein crystal and serial femtosecond crystallography.
Maity B, Shoji M, Luo F, Nakane T, Abe S, Owada S, Kang J, Tono K, Tanaka R, Pham TT, Kojima M, Hishikawa Y, Tanaka J, Tian J, Nagama M, Suzuki T, Noya H, Nakasuji Y, Asanuma A, Yao X, Iwata S, Shigeta Y, Nango E, Ueno T
Nat Commun 15 5518 (2024)
PMID: 38951539

Function and Biology Details

Reaction catalysed: 
Hydrolysis of (1->4)-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrins
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-132831 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Lysozyme C Chain: A
Molecule details ›
Chain: A
Length: 129 amino acids
Theoretical weight: 14.33 KDa
Source organism: Gallus gallus
UniProt:
  • Canonical: P00698 (Residues: 19-147; Coverage: 100%)
Gene name: LYZ
Sequence domains: C-type lysozyme/alpha-lactalbumin family

Ligands and Environments

3 bound ligands:
Ligand CL 1 x CL
Ligand NA 2 x NA
Ligand XTX 1 x XTX
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SACLA BEAMLINE BL2
Spacegroup: P43212
Unit cell:
a: 81.7Å b: 81.7Å c: 37.9Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.194 0.193 0.212

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