21JH | pdb_000021jh

Faecalibacterium duncaniae branching enzyme FdBE2 unliganded form

PDB DOI: https://doi.org/10.2210/pdb21JH/pdb

Classification: TRANSFERASE
Organism(s): Faecalibacterium duncaniae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-12-15 Released: 2025-12-31
Deposition Author(s): Tonozuka, T., Ding, Y., Sugimura, R.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.173 (Depositor), 0.178 (DCC)
R-Value Work:
0.149 (Depositor)
R-Value Observed:
0.150 (Depositor)

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

Literature

Enzymatic and structural and characterization of a branching enzyme FdBE2 from the gut bacterium Faecalibacterium duncaniae

Ding, Y., Sugimura, R., Suzuki, R., Endo, A., Nishikawa, A., Kozono, T., Tonozuka, T.

To be published.

Macromolecule Content

Total Structure Weight: 73.94 kDa
Atom Count: 5,461
Modeled Residue Count: 609
Deposited Residue Count: 637
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1,4-alpha-glucan branching enzyme	A	637	Faecalibacterium duncaniae	Mutation(s): 0 Gene Names: glgB, FAEPRAA2165_01813 EC: 2.4.1.18
UniProt
Find proteins for C7H686 (Faecalibacterium duncaniae (strain DSM 17677 / JCM 31915 / A2-165)) Explore C7H686 Go to UniProtKB: C7H686
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C7H686
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS 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]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] I [auth A] J [auth A] E [auth A], F [auth A], G [auth A], I [auth A], J [auth A], K [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.173 (Depositor), 0.178 (DCC)
R-Value Work: 0.149 (Depositor)
R-Value Observed: 0.150 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 165.84	α = 90
b = 73.988	β = 91.29
c = 57.146	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-12-31

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	24K08698
Japan Society for the Promotion of Science (JSPS)	Japan	24KJ1029

Revision History (Full details and data files)

Version 1.0: 2025-12-31
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.