› 3fbx

X-ray diffraction
2.4Å resolution

Crystal structure of the lysosomal 66.3 kDa protein from mouse solved by S-SAD

Released:
DOI: 10.2210/pdb3fbx/pdb
PDB entry 3fbx coloured by chain, front view.
PDB entry 3fbx coloured by chain, side view.
PDB entry 3fbx coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
De novo sulfur SAD phasing of the lysosomal 66.3 kDa protein from mouse.
Lakomek K, Dickmanns A, Mueller U, Kollmann K, Deuschl F, Berndt A, Lübke T, Ficner R
Acta Crystallogr D Biol Crystallogr 65 220-8 (2009)
PMID: 19237744

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-174812 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Putative phospholipase B-like 2 Chain: A
Molecule details ›
Chain: A
Length: 559 amino acids
Theoretical weight: 63.23 KDa
Source organism: Mus musculus
Expression system: Homo sapiens
UniProt:
  • Canonical: Q3TCN2 (Residues: 47-594; Coverage: 100%)
Gene name: Plbd2
Sequence domains: Phospholipase B
Structure domains: Penicillin V Acylase; Chain A

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
7 bound ligands:
Ligand NAG 3 x NAG
Ligand PG4 2 x PG4
Ligand XE 1 x XE
Ligand GOL 3 x GOL
Ligand ACT 1 x ACT
Ligand PGE 1 x PGE
Ligand NA 1 x NA
1 modified residue:
Ligand OCS 1 x OCS

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.2
Spacegroup: C2
Unit cell:
a: 148.804Å b: 89.672Å c: 64.954Å
α: 90° β: 98.67° γ: 90°
R-values:
R R work R free
0.158 0.156 0.198
Expression system: Homo sapiens

Quick links

Citations

3 citation in other articles

High-resolution structure of a papaya plant-defense barwin-like protein solved by in-house sulfur-SAD phasing.
Huet et al. (2013)
2 more

2 mentions without citation

Carboxylic ester hydrolases: Classification and database derived from their primary, secondary, and tertiary structures.
Chen et al. (2016)
1 more