7sxm

Structure of Xenon-derivatized Methyl-Coenzyme M Reductase from Methanothermobacter marburgensis

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） FACTOR 430 × 2 MAGNESIUM ION × 2 ACETATE ION × 4 Coenzyme B × 2 1-THIOETHANESULFONIC ACID × 2 SODIUM ION × 1 XENON × 8 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 1–548； UniProt 2–549 Author chain D； PDBConstruct 1–548； UniProt 2–549

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） FACTOR 430 × 2 MAGNESIUM ION × 2 ACETATE ION × 4 Coenzyme B × 2 1-THIOETHANESULFONIC ACID × 2 SODIUM ION × 1 XENON × 8 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 1–442； UniProt 2–443 Author chain E； PDBConstruct 1–442； UniProt 2–443

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） FACTOR 430 × 2 MAGNESIUM ION × 2 ACETATE ION × 4 Coenzyme B × 2 1-THIOETHANESULFONIC ACID × 2 SODIUM ION × 1 XENON × 8 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 1–246； UniProt 2–247 Author chain F； PDBConstruct 1–246； UniProt 2–247

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	7sxm
Deposition date deposition_date	2021-11-23
Structure title title	Structure of Xenon-derivatized Methyl-Coenzyme M Reductase from Methanothermobacter marburgensis
Keywords keywords	methyl-coenzyme M reductase, MCR, methanogens, 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.

7sxm__assembly_1__model_1

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

Download this curve (.dat)

7sxm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7sxm__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.36 Å
Rg (electron density)	37.55 Å
Total Rg	37.91 Å
Atom count	19235
Residues	2452
Excluded volume	340630 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7sxm__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 (11)

Entity 1 Entity 1 polymer

Description description	Methyl-coenzyme M reductase I subunit alpha
Molecular weight formula_weight	60377.3 kDa
EC 编号 ec_number	2.8.4.1
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	20235

ADKLFINALKKKFEESPEEKKTTFYTLGGWKQSERKTEFVNAGKEVAAKRGIPQYNPDIGTPLGQRVLMPYQVSTTDTYVEGDDLHFVNNAAMQQMWDDIRRTVIVGLNHAHAVIEKRLGKEVTPETITHYLETVNHAMPGAAVVQEHMVETHPALVADSYVKVFTGNDEIADEIDPAFVIDINKQFPEDQAETLKAEVGDGIWQVVRIPTIVSRTCDGATTSRWSAMQIGMSMISAYKQAAGEAATGDFAYAAKHAEVIHMGTYLPVRRARGENEPGGVPFGYLADICQSSRVNYEDPVRVSLDVVATGAMLYDQIWLGSYMSGGVGFTQYATAAYTDNILDDFTYFGKEYVEDKYGLCEAPNNMDTVLDVATEVTFYGLEQYEEYPALLEDQFGGSQRAAVVAAAAGCSTAFATGNAQTGLSGWYLSMYLHKEQHSRLGFYGYDLQDQCGASNVFSIRGDEGLPLELRGPNYPNYAMNVGHQGEYAGISQAPHAARGDAFVFNPLVKIAFADDNLVFDFTNVRGEFAKGALREFEPAGERALITPA

Entity 2 Entity 2 polymer

Description description	Methyl-coenzyme M reductase I subunit beta
Molecular weight formula_weight	47148.5 kDa
EC 编号 ec_number	2.8.4.1
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

AKFEDKVDLYDDRGNLVEEQVPLEALSPLRNPAIKSIVQGIKRTVAVNLEGIENALKTAKVGGPACKIMGRELDLDIVGNAESIAAAAKEMIQVTEDDDTNVELLGGGKRALVQVPSARFDVAAEYSAAPLVTATAFVQAIINEFDVSMYDANMVKAAVLGRYPQSVEYMGANIATMLDIPQKLEGPGYALRNIMVNHVVAATLKNTLQAAALSTILEQTAMFEMGDAVGAFERMHLLGLAYQGMNADNLVFDLVKANGKEGTVGSVIADLVERALEDGVIKVEKELTDYKVYGTDDLAMWNAYAAAGLMAATMVNQGAARAAQGVSSTLLYYNDLIEFETGLPSVDFGKVEGTAVGFSFFSHSIYGGGGPGIFNGNHIVTRHSKGFAIPCVAAAMALDAGTQMFSPEATSGLIKEVFSQVDEFREPLKYVVEAAAEIKNEI

Entity 3 Entity 3 polymer

Description description	Methyl-coenzyme M reductase I subunit gamma
Molecular weight formula_weight	28423.8 kDa
EC 编号 ec_number	2.8.4.1
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

AQYYPGTTKVAQNRRNFCNPEYELEKLREISDEDVVKILGHRAPGEEYPSVHPPLEEMDEPEDAIREMVEPIDGAKAGDRVRYIQFTDSMYFAPAQPYVRSRAYLCRYRGADAGTLSGRQIIETRERDLEKISKELLETEFFDPARSGVRGKSVHGHSLRLDEDGMMFDMLRRQIYNKDTGRVEMVKNQIGDELDEPVDLGEPLDEETLMEKTTIYRVDGEAYRDDVEAVEIMQRIHVLRSQGGFN

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 non-polymer

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

Entity 8 Entity 8 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 9 Entity 9 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 10 Entity 10 non-polymer

Description description	XENON
Molecular weight formula_weight	131.3 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 11 Entity 11 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	838

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	7sxmB01
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	7sxmE01
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	81.956 Å
Unit-cell length b length_b	115.741 Å
Unit-cell length c length_c	123.400 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.53 °
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	2.503 Å
Low-resolution limit resolution_low	69.630 Å
R factor r_factor	0.1803
R_work r_work	0.1783
R_free r_free	0.2180

Structure of Xenon-derivatized Methyl-Coenzyme M Reductase from Methanothermobacter marburgensis

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

Methyl-coenzyme M reductase I subunit beta

State in the Current Structure

Other States of the Same Protein in the Database

Methyl-coenzyme M reductase I subunit gamma

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7sxm__assembly_1__model_1

7sxm__assembly_1__model_1 | I(q)

7sxm__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 (11)

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 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Structure of Xenon-derivatized Methyl-Coenzyme M Reductase from Methanothermobacter marburgensis

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

7sxm__assembly_1__model_1

7sxm__assembly_1__model_1 | I(q)

7sxm__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 (11)

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 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)