8RIU

Crystal structure of the F420-reducing carbon monoxide dehydrogenase component from the ethanotroph Candidatus Ethanoperedens thermophilum

PDB DOI: https://doi.org/10.2210/pdb8RIU/pdb

Classification: OXIDOREDUCTASE
Organism(s): Candidatus Methanoperedenaceae archaeon GB50
Mutation(s): No

Deposited: 2023-12-19 Released: 2024-10-02
Deposition Author(s): Lemaire, O.N., Wagner, T.
Funding Organization(s): Max Planck Society, German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.187
R-Value Work: 0.165
R-Value Observed: 0.166

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

F420 reduction as a cellular driver for anaerobic ethanotrophy

Lemaire, O.N., Wegener, G., Wagner, T.

To be published.

Macromolecule Content

Total Structure Weight: 304.17 kDa
Atom Count: 21,942
Modelled Residue Count: 2,607
Deposited Residue Count: 2,672
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl-CoA decarbonylase/synthase complex subunit alpha	A, D	792	Candidatus Methanoperedenaceae archaeon GB50	Mutation(s): 0 EC: 1.2.7.4
UniProt
Find proteins for A0A7R9N4A5 (Candidatus Methanoperedenaceae archaeon GB50) Explore A0A7R9N4A5 Go to UniProtKB: A0A7R9N4A5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7R9N4A5
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus	B, E	370	Candidatus Methanoperedenaceae archaeon GB50	Mutation(s): 0
UniProt
Find proteins for A0A7R9R773 (Candidatus Methanoperedenaceae archaeon GB50) Explore A0A7R9R773 Go to UniProtKB: A0A7R9R773
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7R9R773
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl-CoA decarbonylase/synthase complex subunit epsilon	C, F	174	Candidatus Methanoperedenaceae archaeon GB50	Mutation(s): 0
UniProt
Find proteins for A0A7R9N5A2 (Candidatus Methanoperedenaceae archaeon GB50) Explore A0A7R9N5A2 Go to UniProtKB: A0A7R9N5A2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7R9N5A2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 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 EA [auth B] SDF format, chain VA [auth E] MOL2 format, chain EA [auth B] MOL2 format, chain VA [auth E] mmCIF format, chain EA [auth B] mmCIF format, chain VA [auth E]	EA [auth B], VA [auth E]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain EA [auth B] Focus chain VA [auth E] Interactions & Density Focus chain EA [auth B] Focus chain VA [auth E]
XCC (Subject of Investigation/LOI) Query on XCC Download Ideal Coordinates CCD File SDF format, chain PA [auth D] SDF format, chain R [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain R [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain R [auth A]	PA [auth D], R [auth A]	FE(4)-NI(1)-S(4) CLUSTER Fe₄ Ni S₄ QGLWBXDZIHZONR-UHFFFAOYSA-N		Interactions Focus chain PA [auth D] Focus chain R [auth A] Interactions & Density Focus chain PA [auth D] Focus chain R [auth A]
PE4 Query on PE4 Download Ideal Coordinates CCD File SDF format, chain QA [auth D] MOL2 format, chain QA [auth D] mmCIF format, chain QA [auth D]	QA [auth D]	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C₁₆ H₃₄ O₈ PJWQOENWHPEPKI-UHFFFAOYSA-N		Interactions Focus chain QA [auth D] Interactions & Density Focus chain QA [auth D]
SF4 (Subject of Investigation/LOI) Query on SF4 Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain FA [auth B] SDF format, chain MA [auth D] SDF format, chain NA [auth D] SDF format, chain O [auth A] SDF format, chain OA [auth D] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain TA [auth E] SDF format, chain UA [auth E] SDF format, chain WA [auth E] SDF format, chain Y [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain MA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain TA [auth E] MOL2 format, chain UA [auth E] MOL2 format, chain WA [auth E] MOL2 format, chain Y [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain MA [auth D] mmCIF format, chain NA [auth D] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth D] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain TA [auth E] mmCIF format, chain UA [auth E] mmCIF format, chain WA [auth E] mmCIF format, chain Y [auth A]	CA [auth B] DA [auth B] FA [auth B] MA [auth D] NA [auth D] CA [auth B], DA [auth B], FA [auth B], MA [auth D], NA [auth D], O [auth A], OA [auth D], P [auth A], Q [auth A], TA [auth E], UA [auth E], WA [auth E], Y [auth A]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain DA [auth B] Focus chain FA [auth B] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain Q [auth A] Focus chain TA [auth E] Focus chain UA [auth E] Focus chain WA [auth E] Focus chain Y [auth A] Interactions & Density Focus chain CA [auth B] Focus chain DA [auth B] Focus chain FA [auth B] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain Q [auth A] Focus chain TA [auth E] Focus chain UA [auth E] Focus chain WA [auth E] Focus chain Y [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AB [auth F] SDF format, chain G [auth A] SDF format, chain GA [auth B] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain KA [auth D] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain XA [auth E] SDF format, chain YA [auth F] SDF format, chain Z [auth A] MOL2 format, chain AB [auth F] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain KA [auth D] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain XA [auth E] MOL2 format, chain YA [auth F] MOL2 format, chain Z [auth A] mmCIF format, chain AB [auth F] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain HA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain KA [auth D] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A] mmCIF format, chain XA [auth E] mmCIF format, chain YA [auth F] mmCIF format, chain Z [auth A]	AB [auth F] G [auth A] GA [auth B] HA [auth C] IA [auth C] AB [auth F], G [auth A], GA [auth B], HA [auth C], IA [auth C], JA [auth C], KA [auth D], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], XA [auth E], YA [auth F], Z [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AB [auth F] Focus chain G [auth A] Focus chain GA [auth B] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth D] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain XA [auth E] Focus chain YA [auth F] Focus chain Z [auth A] Interactions & Density Focus chain AB [auth F] Focus chain G [auth A] Focus chain GA [auth B] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth D] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain XA [auth E] Focus chain YA [auth F] Focus chain Z [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain LA [auth D] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain X [auth A] SDF format, chain ZA [auth F] MOL2 format, chain BA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain X [auth A] MOL2 format, chain ZA [auth F] mmCIF format, chain BA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain X [auth A] mmCIF format, chain ZA [auth F]	BA [auth B] H [auth A] I [auth A] J [auth A] K [auth A] BA [auth B], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], LA [auth D], M [auth A], N [auth A], X [auth A], ZA [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain N [auth A] Focus chain X [auth A] Focus chain ZA [auth F] Interactions & Density Focus chain BA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain N [auth A] Focus chain X [auth A] Focus chain ZA [auth F]
K Query on K Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain SA [auth D] MOL2 format, chain AA [auth A] MOL2 format, chain SA [auth D] mmCIF format, chain AA [auth A] mmCIF format, chain SA [auth D]	AA [auth A], SA [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain SA [auth D] Interactions & Density Focus chain AA [auth A] Focus chain SA [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain RA [auth D] MOL2 format, chain RA [auth D] mmCIF format, chain RA [auth D]	RA [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain RA [auth D] Interactions & Density Focus chain RA [auth D]