› 5m17

X-ray diffraction
1.03Å resolution

Structure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with mannose-alpha-1,3-1,2-dideoxymannose

Released:
DOI: 10.2210/pdb5m17/pdb
PDB entry 5m17 coloured by chain, front view.
PDB entry 5m17 coloured by chain, side view.
PDB entry 5m17 coloured by chain, top view.
Source organism: Bacteroides xylanisolvens XB1A
Primary publication:
Contribution of Shape and Charge to the Inhibition of a Family GH99 endo-α-1,2-Mannanase.
Petricevic M, Sobala LF, Fernandes PZ, Raich L, Thompson AJ, Bernardo-Seisdedos G, Millet O, Zhu S, Sollogoub M, Jiménez-Barbero J, Rovira C, Davies GJ, Williams SJ
J Am Chem Soc 139 1089-1097 (2017)
PMID: 27992199

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-112767 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Glycosyl hydrolase family 71 Chain: A
Molecule details ›
Chain: A
Length: 385 amino acids
Theoretical weight: 43.93 KDa
Source organism: Bacteroides xylanisolvens XB1A
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: D6D1V7 (Residues: 17-380; Coverage: 96%)
Gene name: BXY_34140
Sequence domains: Glycosyl hydrolase family 99
Structure domains: Glycosidases

Ligands and Environments

Carbohydrate polymer : NEW Components: 7D1, MAN
Carbohydrate polymer
2 bound ligands:
Ligand EDO 2 x EDO
Ligand ACT 1 x ACT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: I4
Unit cell:
a: 108.576Å b: 108.576Å c: 67.746Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.117 0.117 0.13
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

7 citation in other articles

Unraveling the structural and chemical features of biological short hydrogen bonds.
Zhou et al. (2019)
6 more

2 mentions without citation

Blooms of single bacterial species in a coastal lagoon of the southwestern Atlantic Ocean.
Piccini et al. (2006)
1 more