7b2h

Crystal structure of the methyl-coenzyme M reductase from Methanothermobacter Marburgensis derivatized with xenon

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Methyl-coenzyme M reductase I subunit alpha

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Methyl-coenzyme M reductase I subunit beta × 2 （P11560） Methyl-coenzyme M reductase I subunit gamma × 2 （P11562） 1-THIOETHANESULFONIC ACID × 2 Coenzyme B × 2 POTASSIUM ION × 4 DI(HYDROXYETHYL)ETHER × 9 GLYCEROL × 1 1,2-ETHANEDIOL × 1 FACTOR 430 × 2 MAGNESIUM ION × 15 XENON × 12 SULFATE ION × 1 CHLORIDE ION × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MCRA_METTM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–550； UniProt 1–550 Author chain D； PDBConstruct 1–550； UniProt 1–550

Methyl-coenzyme M reductase I subunit beta

OrganismNot specified

UniProt P11560

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Methyl-coenzyme M reductase I subunit alpha × 2 （P11558） Methyl-coenzyme M reductase I subunit gamma × 2 （P11562） 1-THIOETHANESULFONIC ACID × 2 Coenzyme B × 2 POTASSIUM ION × 4 DI(HYDROXYETHYL)ETHER × 9 GLYCEROL × 1 1,2-ETHANEDIOL × 1 FACTOR 430 × 2 MAGNESIUM ION × 15 XENON × 12 SULFATE ION × 1 CHLORIDE ION × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MCRB_METTM
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–443； UniProt 1–443 Author chain E； PDBConstruct 1–443； UniProt 1–443

Methyl-coenzyme M reductase I subunit gamma

OrganismNot specified

UniProt P11562

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Methyl-coenzyme M reductase I subunit alpha × 2 （P11558） Methyl-coenzyme M reductase I subunit beta × 2 （P11560） 1-THIOETHANESULFONIC ACID × 2 Coenzyme B × 2 POTASSIUM ION × 4 DI(HYDROXYETHYL)ETHER × 9 GLYCEROL × 1 1,2-ETHANEDIOL × 1 FACTOR 430 × 2 MAGNESIUM ION × 15 XENON × 12 SULFATE ION × 1 CHLORIDE ION × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MCRG_METTM
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–249； UniProt 1–249 Author chain F； PDBConstruct 1–249； UniProt 1–249

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7b2h
Deposition date deposition_date	2020-11-27
Structure title title	Crystal structure of the methyl-coenzyme M reductase from Methanothermobacter Marburgensis derivatized with xenon
Keywords keywords	;Ethyl-CoM reductase, Methyl-CoM reductase, xenon-derivatization, F430-cofactor, post-translational modification, coenzyme M, coenzyme B, thermophile, archaea., TRANSFERASE ;; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

7b2h__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

7b2h__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7b2h__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	38.20 Å
Rg (electron density)	37.38 Å
Total Rg	37.72 Å
Atom count	19211
Residues	2453
Excluded volume	340560 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7b2h__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (15)

Entity 1 Entity 1 polymer

Description description	Methyl-coenzyme M reductase I subunit alpha
Molecular weight formula_weight	60637.6 kDa
EC 编号 ec_number	2.8.4.1
Mutation mutation	wild-type
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	20066

MADKLFINALKKKFEESPEEKKTTFYTLGGWKQSERKTEFVNAGKEVAAKRGIPQYNPDIGTPLGQRVLMPYQVSTTDTYVEGDDLHFVNNAAMQQMWDDIRRTVIVGLNHAHAVIEKRLGKEVTPETITHYLETVNHAMPGAAVVQEHMVETHPALVADSYVKVFTGNDEIADEIDPAFVIDINKQFPEDQAETLKAEVGDGIWQVVRIPTIVSRTCDGATTSRWSAMQIGMSMISAYKQAAGEAATGDFAYAAKHAEVIHMGTYLPVRRARGENEPGGVPFGYLADICQSSRVNYEDPVRVSLDVVATGAMLYDQIWLGSYMSGGVGFTQYATAAYTDNILDDFTYFGKEYVEDKYGLCEAPNNMDTVLDVATEVTFYGLEQYEEYPALLEDQFGGSQRAAVVAAAAGCSTAFATGNAQTGLSGWYLSMYLHKEQHSRLGFYGYDLQDQCGASNVFSIRGDEGLPLELRGPNYPNYAMNVGHQGEYAGISQAPHAARGDAFVFNPLVKIAFADDNLVFDFTNVRGEFAKGALREFEPAGERALITPAK

Entity 2 Entity 2 polymer

Description description	Methyl-coenzyme M reductase I subunit beta
Molecular weight formula_weight	47279.7 kDa
EC 编号 ec_number	2.8.4.1
Mutation mutation	wild-type
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E

MAKFEDKVDLYDDRGNLVEEQVPLEALSPLRNPAIKSIVQGIKRTVAVNLEGIENALKTAKVGGPACKIMGRELDLDIVGNAESIAAAAKEMIQVTEDDDTNVELLGGGKRALVQVPSARFDVAAEYSAAPLVTATAFVQAIINEFDVSMYDANMVKAAVLGRYPQSVEYMGANIATMLDIPQKLEGPGYALRNIMVNHVVAATLKNTLQAAALSTILEQTAMFEMGDAVGAFERMHLLGLAYQGMNADNLVFDLVKANGKEGTVGSVIADLVERALEDGVIKVEKELTDYKVYGTDDLAMWNAYAAAGLMAATMVNQGAARAAQGVSSTLLYYNDLIEFETGLPSVDFGKVEGTAVGFSFFSHSIYGGGGPGIFNGNHIVTRHSKGFAIPCVAAAMALDAGTQMFSPEATSGLIKEVFSQVDEFREPLKYVVEAAAEIKNEI

Entity 3 Entity 3 polymer

Description description	Methyl-coenzyme M reductase I subunit gamma
Molecular weight formula_weight	28797.2 kDa
EC 编号 ec_number	2.8.4.1
Mutation mutation	wild-type
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F

MAQYYPGTTKVAQNRRNFCNPEYELEKLREISDEDVVKILGHRAPGEEYPSVHPPLEEMDEPEDAIREMVEPIDGAKAGDRVRYIQFTDSMYFAPAQPYVRSRAYLCRYRGADAGTLSGRQIIETRERDLEKISKELLETEFFDPARSGVRGKSVHGHSLRLDEDGMMFDMLRRQIYNKDTGRVEMVKNQIGDELDEPVDLGEPLDEETLMEKTTIYRVDGEAYRDDVEAVEIMQRIHVLRSQGGFNLE

Entity 4 Entity 4 non-polymer

Description description	1-THIOETHANESULFONIC ACID
Molecular weight formula_weight	142.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	Coenzyme B
Molecular weight formula_weight	343.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 8 Entity 8 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 10 Entity 10 non-polymer

Description description	FACTOR 430
Molecular weight formula_weight	906.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 11 Entity 11 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	15

Entity 12 Entity 12 non-polymer

Description description	XENON
Molecular weight formula_weight	131.3 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 13 Entity 13 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 14 Entity 14 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 15 Entity 15 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	772

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d7b2ha1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.31 — Methyl-coenzyme M reductase subunits
Family Family family	d.58.31.2 — Methyl-coenzyme M reductase alpha and beta chain N-terminal domain

Domain ID domain_id	d7b2ha2
Class class	a — All alpha proteins
Fold Fold fold	a.89 — Methyl-coenzyme M reductase alpha and beta chain C-terminal domain
Superfamily Superfamily superfamily	a.89.1 — Methyl-coenzyme M reductase alpha and beta chain C-terminal domain
Family Family family	a.89.1.1 — Methyl-coenzyme M reductase alpha and beta chain C-terminal domain

Domain ID domain_id	d7b2hb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.31 — Methyl-coenzyme M reductase subunits
Family Family family	d.58.31.2 — Methyl-coenzyme M reductase alpha and beta chain N-terminal domain

Domain ID domain_id	d7b2hb2
Class class	a — All alpha proteins
Fold Fold fold	a.89 — Methyl-coenzyme M reductase alpha and beta chain C-terminal domain
Superfamily Superfamily superfamily	a.89.1 — Methyl-coenzyme M reductase alpha and beta chain C-terminal domain
Family Family family	a.89.1.1 — Methyl-coenzyme M reductase alpha and beta chain C-terminal domain

Domain ID domain_id	d7b2hc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.31 — Methyl-coenzyme M reductase subunits
Family Family family	d.58.31.1 — Methyl-coenzyme M reductase gamma chain

Domain ID domain_id	d7b2hd1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.31 — Methyl-coenzyme M reductase subunits
Family Family family	d.58.31.2 — Methyl-coenzyme M reductase alpha and beta chain N-terminal domain

Domain ID domain_id	d7b2hd2
Class class	a — All alpha proteins
Fold Fold fold	a.89 — Methyl-coenzyme M reductase alpha and beta chain C-terminal domain
Superfamily Superfamily superfamily	a.89.1 — Methyl-coenzyme M reductase alpha and beta chain C-terminal domain
Family Family family	a.89.1.1 — Methyl-coenzyme M reductase alpha and beta chain C-terminal domain

Domain ID domain_id	d7b2he1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.31 — Methyl-coenzyme M reductase subunits
Family Family family	d.58.31.2 — Methyl-coenzyme M reductase alpha and beta chain N-terminal domain

Domain ID domain_id	d7b2he2
Class class	a — All alpha proteins
Fold Fold fold	a.89 — Methyl-coenzyme M reductase alpha and beta chain C-terminal domain
Superfamily Superfamily superfamily	a.89.1 — Methyl-coenzyme M reductase alpha and beta chain C-terminal domain
Family Family family	a.89.1.1 — Methyl-coenzyme M reductase alpha and beta chain C-terminal domain

Domain ID domain_id	d7b2hf_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.31 — Methyl-coenzyme M reductase subunits
Family Family family	d.58.31.1 — Methyl-coenzyme M reductase gamma chain

CATH v4.4 (2 domains)

Domain ID domain_id	7b2hB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	470 —

Domain ID domain_id	7b2hE01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	470 —

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Unit-cell length a length_a	81.719 Å
Unit-cell length b length_b	116.386 Å
Unit-cell length c length_c	123.070 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.36 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.120 Å
Low-resolution limit resolution_low	48.170 Å
R factor r_factor	0.1786
R_work r_work	0.1772
R_free r_free	0.2042

Crystal structure of the methyl-coenzyme M reductase from Methanothermobacter Marburgensis derivatized with xenon

1. Protein Identity and Related Structures Protein Identity & Related Structures

Methyl-coenzyme M reductase I subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Methyl-coenzyme M reductase I subunit beta

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Methyl-coenzyme M reductase I subunit gamma

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7b2h__assembly_1__model_1

7b2h__assembly_1__model_1 | I(q)

7b2h__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (15)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 non-polymer

Entity 13 Entity 13 non-polymer

Entity 14 Entity 14 non-polymer

Entity 15 Entity 15 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (10 domains)

CATH v4.4 (2 domains)

7. Citations (1)