5N6U

Crystal structure of Beta-D-Mannosidase from Dictyoglomus thermophilum.

• PDB DOI: https://doi.org/10.2210/pdb5N6U/pdb

• Classification: HYDROLASE
• Organism(s): Dictyoglomus thermophilum H-6-12
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-02-16 Released: 2017-04-12 
• Deposition Author(s): Richet, N., Lafite, P.
• Funding Organization(s): GLYCOPEPS

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.08 Å
• R-Value Free: 0.255 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 395.49 kDa 
• Atom Count: 27,265 
• Modelled Residue Count: 3,244 
• Deposited Residue Count: 3,344 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-mannosidase	A, B, C, D	836	Dictyoglomus thermophilum H-6-12	Mutation(s): 1  Gene Names: DICTH_1692 EC: 3.2.1.25
UniProt
Find proteins for B5YAN4 (Dictyoglomus thermophilum (strain ATCC 35947 / DSM 3960 / H-6-12)) Explore B5YAN4  Go to UniProtKB:  B5YAN4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BMA	E [auth A], F [auth B], G [auth C], H [auth D]	beta-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.08 Å
• R-Value Free: 0.255 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.25	α = 90
b = 75.56	β = 92.52
c = 217.88	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
MOLREP	phasing
Aimless	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-04-12 
Deposition Author(s): Richet, N., Lafite, P.

---

Funding Organization	Location	Grant Number
GLYCOPEPS	France	APR-518N

Revision History  

• Version 1.0: 2017-04-12
  Type: Initial release
  
• Version 1.1: 2017-04-19
  Changes: Database references
• Version 1.2: 2017-05-17
  Changes: Database references
• Version 1.3: 2019-02-20
  Changes: Advisory, Data collection, Derived calculations
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.5: 2024-01-17
  Changes: Data collection, Database references, Refinement description, Structure summary