9GMJ | pdb_00009gmj

The crystal structure of ManDH5 Selenomethionine derivative at 1.6 Angstroms resolution - a beta-D-Mannanase of GH5 family from Dictyoglomus thermophilium

• PDB DOI: https://doi.org/10.2210/pdb9GMJ/pdb

• Classification: HYDROLASE
• Organism(s): Dictyoglomus thermophilum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-08-28 Released: 2025-09-10 
• Deposition Author(s): Sivron, Y., Romano, A., Shoham, Y., Shoham, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.190 (Depositor), 0.191 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Literature

The crystal structure of ManDH5 Selenomethionine derivative at 1.6 Angstroms Resolution - a beta-D-Mannanase of GH5 family from Dictyoglomus thermophilium

Sivron, Y., Romano, A., Shoham, Y., Shoham, G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 67.9 kDa 
• Atom Count: 5,168 
• Modeled Residue Count: 561 
• Deposited Residue Count: 568 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DUF5060 domain-containing protein	A	568	Dictyoglomus thermophilum	Mutation(s): 0  Gene Names: ENW00_02810
UniProt
Find proteins for A0A7C3MIF0 (Dictyoglomus thermophilum) Explore A0A7C3MIF0  Go to UniProtKB:  A0A7C3MIF0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	C [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.190 (Depositor), 0.191 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.207	α = 90
b = 99.274	β = 90
c = 153.724	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
xia2	data scaling
CRANK2	phasing
BUCCANEER	model building
PHENIX	refinement
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2025-09-10 
Deposition Author(s): Sivron, Y., Romano, A., Shoham, Y., Shoham, G.

Revision History  

• Version 1.0: 2025-09-10
  Type: Initial release