9GPD | pdb_00009gpd

ManDH5 E303Q mutant in complex with mannotriose a beta-D-Mannanase of GH5 family from Dictyoglomus thermophilium

PDB DOI: https://doi.org/10.2210/pdb9GPD/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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free:
0.167 (Depositor), 0.171 (DCC)
R-Value Work:
0.156 (Depositor), 0.159 (DCC)
R-Value Observed:
0.156 (Depositor)

Starting Model: experimental
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This is version 1.0 of the entry. See complete history.

Literature

ManDH5 E303Q mutant in complex with mannotriose, a beta-D-Mannanase of GH5 family from Dictyoglomus thermophilium

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

To be published.

Macromolecule Content

Total Structure Weight: 67.91 kDa
Atom Count: 5,492
Modeled Residue Count: 563
Deposited Residue Count: 568
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A7C3MIF0
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose	B	3		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G26320VF GlyCosmos: G26320VF GlyGen: G26320VF

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.167 (Depositor), 0.171 (DCC)
R-Value Work: 0.156 (Depositor), 0.159 (DCC)
R-Value Observed: 0.156 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.785	α = 90
b = 99.114	β = 90
c = 153.841	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-09-17

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.