7W2J

Cryo-EM Structure of Membrane-bound Fructose Dehydrogenase from Gluconobacter japonicus

PDB DOI: https://doi.org/10.2210/pdb7W2J/pdb
EM Map EMD-32262: EMDB EMDataResource

Classification: OXIDOREDUCTASE
Organism(s): Gluconobacter japonicus
Expression System: Gluconobacter oxydans
Mutation(s): No

Deposited: 2021-11-24 Released: 2022-11-30
Deposition Author(s): Suzuki, Y., Makino, F., Miyata, T., Tanaka, H., Namba, K., Sowa, K., Kitazumi, Y., Shirai, O.
Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Essential Insight of Direct Electron Transfer-Type Bioelectrocatalysis by Membrane-Bound d-Fructose Dehydrogenase with Structural Bioelectrochemistry

Suzuki, Y., Makino, F., Miyata, T., Tanaka, H., Namba, K., Kano, K., Sowa, K., Kitazumi, Y., Shirai, O.

(2023) ACS Catal 13: 13828-13837

DOI: https://doi.org/10.1021/acscatal.3c03769

Macromolecule Content

Total Structure Weight: 270.19 kDa
Atom Count: 16,522
Modelled Residue Count: 2,104
Deposited Residue Count: 2,426
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fructose dehydrogenase large subunit	A, D	544	Gluconobacter japonicus	Mutation(s): 0 Gene Names: fdhL EC: 1.1.99.11
UniProt
Find proteins for M1VMF7 (Gluconobacter japonicus) Explore M1VMF7 Go to UniProtKB: M1VMF7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	M1VMF7
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fructose dehydrogenase small subunit	B, E	183	Gluconobacter japonicus	Mutation(s): 0 Gene Names: fdhS
UniProt
Find proteins for M1VB40 (Gluconobacter japonicus) Explore M1VB40 Go to UniProtKB: M1VB40
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	M1VB40
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fructose dehydrogenase cytochrome subunit	C, F	486	Gluconobacter japonicus	Mutation(s): 0 Gene Names: fdhC
UniProt
Find proteins for M1V1V5 (Gluconobacter japonicus) Explore M1V1V5 Go to UniProtKB: M1V1V5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	M1V1V5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth D] MOL2 format, chain G [auth A] MOL2 format, chain L [auth D]	G [auth A], L [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain G [auth A] Focus chain L [auth D] Interactions & Density Focus chain G [auth A] Focus chain L [auth D]
HEC (Subject of Investigation/LOI) Query on HEC Download Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain N [auth F] SDF format, chain O [auth F] SDF format, chain P [auth F] MOL2 format, chain I [auth C] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain N [auth F] MOL2 format, chain O [auth F] MOL2 format, chain P [auth F]	I [auth C] J [auth C] K [auth C] N [auth F] O [auth F] I [auth C], J [auth C], K [auth C], N [auth F], O [auth F], P [auth F]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth C] Focus chain N [auth F] Focus chain O [auth F] Focus chain P [auth F] Interactions & Density Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth C] Focus chain N [auth F] Focus chain O [auth F] Focus chain P [auth F]
F3S Query on F3S Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain M [auth D] MOL2 format, chain H [auth A] MOL2 format, chain M [auth D]	H [auth A], M [auth D]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain M [auth D] Interactions & Density Focus chain H [auth A] Focus chain M [auth D]