9QR1 | pdb_00009qr1

Methyl-coenzyme M reductase of ANME-2d Candidatus Methanoperedens sp. BLZ2 from a bioreactor enrichment culture

PDB DOI: https://doi.org/10.2210/pdb9QR1/pdb

Classification: TRANSFERASE
Organism(s): Candidatus Methanoperedens sp. BLZ2
Mutation(s): No

Deposited: 2025-04-02 Released: 2025-07-16
Deposition Author(s): Mueller, M.-C., Wagner, T.
Funding Organization(s): European Research Council (ERC), German Research Foundation (DFG), Netherlands Organisation for Scientific Research (NWO), Max Planck Society

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 0.98 Å
R-Value Free:
0.118 (Depositor), 0.133 (DCC)
R-Value Work:
0.102 (Depositor), 0.125 (DCC)
R-Value Observed:
0.103 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Atomic resolution structures of the key enzyme MCR in anaerobic methanotrophy reveal novel and extensive post-translational modifications.

Mueller, M.-C., Wissink, M., Mukherjee, P., von Possel, N., Laso-Perez, R., Engilberge, S., Carpentier, P., Kahnt, J., Wegener, G., Welte, C.U., Wagner, T.

To be published.

Macromolecule Content

Total Structure Weight: 274.7 kDa
Atom Count: 23,357
Modeled Residue Count: 2,483
Deposited Residue Count: 2,491
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyl-coenzyme M reductase subunit alpha	A, D	562	Candidatus Methanoperedens sp. BLZ2	Mutation(s): 0 EC: 2.8.4.1
UniProt
Find proteins for A0A6A2FLY3 (Candidatus Methanoperedens sp) Explore A0A6A2FLY3 Go to UniProtKB: A0A6A2FLY3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A6A2FLY3
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyl-coenzyme M reductase subunit beta	B, E	434	Candidatus Methanoperedens sp. BLZ2	Mutation(s): 0 EC: 2.8.4.1
UniProt
Find proteins for A0A6A2G3Q8 (Candidatus Methanoperedens sp) Explore A0A6A2G3Q8 Go to UniProtKB: A0A6A2G3Q8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A6A2G3Q8
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
coenzyme-B sulfoethylthiotransferase	C, F	249	Candidatus Methanoperedens sp. BLZ2	Mutation(s): 0 EC: 2.8.4.1
UniProt
Find proteins for A0A5E4HJB0 (Uncultured archaeon) Explore A0A5E4HJB0 Go to UniProtKB: A0A5E4HJB0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A5E4HJB0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
F43 (Subject of Investigation/LOI) Query on F43 Download Ideal Coordinates CCD File SDF format, chain HA [auth D] SDF format, chain M [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain M [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain M [auth A]	HA [auth D], M [auth A]	FACTOR 430 C₄₂ H₅₁ N₆ Ni O₁₃ XLFIRMYGVLUNOY-SXMZNAGASA-M		Interactions Focus chain HA [auth D] Focus chain M [auth A] Interactions & Density Focus chain HA [auth D] Focus chain M [auth A]
TP7 (Subject of Investigation/LOI) Query on TP7 Download Ideal Coordinates CCD File SDF format, chain IA [auth D] SDF format, chain O [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain O [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain O [auth A]	IA [auth D], O [auth A]	Coenzyme B C₁₁ H₂₂ N O₇ P S JBJSVEVEEGOEBZ-SCZZXKLOSA-N		Interactions Focus chain IA [auth D] Focus chain O [auth A] Interactions & Density Focus chain IA [auth D] Focus chain O [auth A]
COM (Subject of Investigation/LOI) Query on COM Download Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain P [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain P [auth A] mmCIF format, chain EA [auth D] mmCIF format, chain P [auth A]	EA [auth D], P [auth A]	1-THIOETHANESULFONIC ACID C₂ H₆ O₃ S₂ ZNEWHQLOPFWXOF-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Focus chain P [auth A] Interactions & Density Focus chain EA [auth D] Focus chain P [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain L [auth A] SDF format, chain N [auth A] SDF format, chain R [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain Z [auth C] SDF format, chain AA [auth C] SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain GA [auth D] SDF format, chain J [auth A] SDF format, chain KA [auth E] SDF format, chain LA [auth E] SDF format, chain NA [auth F] SDF format, chain OA [auth F] SDF format, chain S [auth B] SDF format, chain V [auth B] SDF format, chain X [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth A] MOL2 format, chain R [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain KA [auth E] MOL2 format, chain LA [auth E] MOL2 format, chain NA [auth F] MOL2 format, chain OA [auth F] MOL2 format, chain S [auth B] MOL2 format, chain V [auth B] MOL2 format, chain X [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth A] mmCIF format, chain N [auth A] mmCIF format, chain R [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain KA [auth E] mmCIF format, chain LA [auth E] mmCIF format, chain NA [auth F] mmCIF format, chain OA [auth F] mmCIF format, chain S [auth B] mmCIF format, chain V [auth B] mmCIF format, chain X [auth B]	AA [auth C] BA [auth D] CA [auth D] DA [auth D] GA [auth D] AA [auth C], BA [auth D], CA [auth D], DA [auth D], GA [auth D], H [auth A], I [auth A], J [auth A], KA [auth E], L [auth A], LA [auth E], N [auth A], NA [auth F], OA [auth F], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], X [auth B], Z [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain GA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain KA [auth E] Focus chain L [auth A] Focus chain LA [auth E] Focus chain N [auth A] Focus chain NA [auth F] Focus chain OA [auth F] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain X [auth B] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain GA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain KA [auth E] Focus chain L [auth A] Focus chain LA [auth E] Focus chain N [auth A] Focus chain NA [auth F] Focus chain OA [auth F] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain X [auth B] Focus chain Z [auth C]
NO3 Query on NO3 Download Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain K [auth A] SDF format, chain MA [auth E] SDF format, chain W [auth B] SDF format, chain Y [auth B] MOL2 format, chain FA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain MA [auth E] MOL2 format, chain W [auth B] MOL2 format, chain Y [auth B] mmCIF format, chain FA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain MA [auth E] mmCIF format, chain W [auth B] mmCIF format, chain Y [auth B]	FA [auth D], K [auth A], MA [auth E], W [auth B], Y [auth B]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain FA [auth D] Focus chain K [auth A] Focus chain MA [auth E] Focus chain W [auth B] Focus chain Y [auth B] Interactions & Density Focus chain FA [auth D] Focus chain K [auth A] Focus chain MA [auth E] Focus chain W [auth B] Focus chain Y [auth B]
K Query on K Download Ideal Coordinates CCD File SDF format, chain JA [auth E] SDF format, chain Q [auth B] MOL2 format, chain JA [auth E] MOL2 format, chain Q [auth B] mmCIF format, chain JA [auth E] mmCIF format, chain Q [auth B]	JA [auth E], Q [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain JA [auth E] Focus chain Q [auth B] Interactions & Density Focus chain JA [auth E] Focus chain Q [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Modified Residues 8 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AGM Query on AGM	A, D	L-PEPTIDE LINKING	C₇ H₁₇ N₄ O₂		ARG
CSO Query on CSO	A, D	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS
DYA Query on DYA	A, D	L-PEPTIDE LINKING	C₄ H₅ N O₄		ASP
GL3 Query on GL3	A, D	L-PEPTIDE LINKING	C₂ H₅ N O S		GLY
MHS Query on MHS	A, D	L-PEPTIDE LINKING	C₇ H₁₁ N₃ O₂		HIS
SMC Query on SMC	A, D	L-PEPTIDE LINKING	C₄ H₉ N O₂ S		CYS
TRX Query on TRX	A, D	L-PEPTIDE LINKING	C₁₁ H₁₂ N₂ O₃		TRP
A1I9G Query on A1I9G	C, F	L-PEPTIDE LINKING	C₇ H₁₁ N₃ O₂		HIS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 0.98 Å
R-Value Free: 0.118 (Depositor), 0.133 (DCC)
R-Value Work: 0.102 (Depositor), 0.125 (DCC)
R-Value Observed: 0.103 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.575	α = 90
b = 189.299	β = 114.27
c = 84.109	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
STARANISO	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-07-16

Deposition Author(s):

Mueller, M.-C.

Wagner, T.

Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	101125699
German Research Foundation (DFG)	Germany	WA 4053/1-1
Netherlands Organisation for Scientific Research (NWO)	Netherlands	VI.Vidi.223.012
Netherlands Organisation for Scientific Research (NWO)	Netherlands	024.002.002
Max Planck Society	Germany	--