9FMG | pdb_00009fmg

Methylthio-alkane reductase complex

PDB DOI: https://doi.org/10.2210/pdb9FMG/pdb
EM Map EMD-50553: EMDB EMDataResource

Classification: OXIDOREDUCTASE
Organism(s): Rhodospirillum rubrum
Expression System: Rhodobacter capsulatus
Mutation(s): No

Deposited: 2024-06-06 Released: 2025-09-17
Deposition Author(s): Lago-Maciel, A., Zarzycki, J., Prinz, S., Reif-Trauttmansdorff, T., Rebelein, J.G.
Funding Organization(s): German Research Foundation (DFG), Max Planck Society

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.71 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

Structural characterization of the methylthio-alkane reductase from the nitrogenase family

Lago-Maciel, A., Soares, J., Zarzycki, J., Prinz, S., Reif-Trattmansdorff, T., Schuller, J.M., Paczia, N., Pierik, A.J., Rebelein, J.G.

To be published.

Macromolecule Content

Total Structure Weight: 225.94 kDa
Atom Count: 13,763
Modeled Residue Count: 1,768
Deposited Residue Count: 2,045
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase	A	519	Rhodospirillum rubrum	Mutation(s): 0 Gene Names: Rru_A0794 EC: 1.18.6.1
UniProt
Find proteins for Q2RW97 (Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1)) Explore Q2RW97 Go to UniProtKB: Q2RW97
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2RW97
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase	B, C	466	Rhodospirillum rubrum	Mutation(s): 0 Gene Names: Rru_A0793 EC: 1.18.6.1
UniProt
Find proteins for Q2RW98 (Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1)) Explore Q2RW98 Go to UniProtKB: Q2RW98
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2RW98
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogenase iron protein	D, E	297	Rhodospirillum rubrum	Mutation(s): 0 Gene Names: nifH, Rru_A0795 EC: 1.18.6.1
UniProt
Find proteins for Q2RW96 (Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1)) Explore Q2RW96 Go to UniProtKB: Q2RW96
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2RW96
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
S5Q (Subject of Investigation/LOI) Query on S5Q Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	FeFe cofactor C Fe₈ S₉ ARHQIUGQOSHZFD-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
CLF (Subject of Investigation/LOI) Query on CLF Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	FE(8)-S(7) CLUSTER Fe₈ S₇ JKVMXLBGZBULKV-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain L [auth E] MOL2 format, chain H [auth D] MOL2 format, chain L [auth E] mmCIF format, chain H [auth D] mmCIF format, chain L [auth E]	H [auth D], L [auth E]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain H [auth D] Focus chain L [auth E] Interactions & Density Focus chain H [auth D] Focus chain L [auth E]
SF4 (Subject of Investigation/LOI) Query on SF4 Download Ideal Coordinates CCD File SDF format, chain K [auth D] MOL2 format, chain K [auth D] mmCIF format, chain K [auth D]	K [auth D]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain K [auth D] Interactions & Density Focus chain K [auth D]
AF3 Query on AF3 Download Ideal Coordinates CCD File SDF format, chain J [auth D] SDF format, chain N [auth E] MOL2 format, chain J [auth D] MOL2 format, chain N [auth E] mmCIF format, chain J [auth D] mmCIF format, chain N [auth E]	J [auth D], N [auth E]	ALUMINUM FLUORIDE Al F₃ KLZUFWVZNOTSEM-UHFFFAOYSA-K		Interactions Focus chain J [auth D] Focus chain N [auth E] Interactions & Density Focus chain J [auth D] Focus chain N [auth E]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain M [auth E] SDF format, chain I [auth D] MOL2 format, chain M [auth E] MOL2 format, chain I [auth D] mmCIF format, chain M [auth E] mmCIF format, chain I [auth D]	I [auth D], M [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth D] Focus chain M [auth E] Interactions & Density Focus chain I [auth D] Focus chain M [auth E]