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.

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)

wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

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.

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

Find similar proteins by:

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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

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Entry History

Deposition Data

Released Date: 2025-09-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2025-09-10
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.