9GPF | pdb_00009gpf

ManDH5 E303Q in complex with mannopentaose after co-crystalliztion with mannopentaose at 1.6 angstroms resolution a beta-D-Mannanase of GH5 family from Dictyoglomus thermophilium

• PDB DOI: https://doi.org/10.2210/pdb9GPF/pdb

• Classification: HYDROLASE
• Organism(s): Dictyoglomus thermophilum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-09-07 Released: 2025-09-17 
• Deposition Author(s): Sivron, Y., Romano, A., Shoham, Y., Shoham, G.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.174 (Depositor), 0.177 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.160 (Depositor) 

Starting Model: experimental

Literature

ManDH5 E303Q in complex with mannopentaose after co-crystalliztion with mannopentaose 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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 68.85 kDa 
• Atom Count: 5,425 
• Modeled Residue Count: 563 
• 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): 1  Gene Names: ENW00_02810
UniProt
Find proteins for A0A7C3MIF0 (Dictyoglomus thermophilum) Explore A0A7C3MIF0  Go to UniProtKB:  A0A7C3MIF0

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-beta-D-mannopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan:  G78317QO GlyCosmos:  G78317QO GlyGen:  G78317QO

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose	C	5		N/A
Glycosylation Resources
GlyTouCan:  G91924WY GlyCosmos:  G91924WY GlyGen:  G91924WY

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A], E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 2 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900115	B	4beta-beta-mannobiose	Oligosaccharide / Metabolism

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900016	C	beta-cellopentaose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.174 (Depositor), 0.177 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.568	α = 90
b = 98.902	β = 90
c = 153.246	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-17 
Deposition Author(s): Sivron, Y., Romano, A., Shoham, Y., Shoham, G.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-09-17
  Type: Initial release