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9qr1

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

Method: X-RAY DIFFRACTION D_max: 121.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qr1
deposition_date	2025-04-02
title	Methyl-coenzyme M reductase of ANME-2d Candidatus Methanoperedens sp. BLZ2 from a bioreactor enrichment culture
keywords	;methanotrophy, anaerobic methanotrophic archaea, methane oxidation, ANME, methyl-coenzyme M reductase, MCR, reverse methanogenesis, nickel-dependent enzyme, coenzyme M, coenzyme B, F430 cofactor, TRANSFERASE ;; TRANSFERASE
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	37.99 Å
rg_electron	37.37 Å
i0	1149550000.00
molecular_weight	272920.0 kDa
excluded_volume	338550 Å³
envelope_volume	383230 Å³
shell_volume	79024 Å³
envelope_diameter	128.4 Å
shell_rg	47.33 Å
envelope_rg	37.63 Å
shape_rg	37.48 Å
total_rg	37.46 Å
total_atoms	37732
n_residues	2466
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	121.2 Å
rg_real	37.81 Å
rg_real_error	0.53 Å
i0_real	1.1500e+09
i0_real_error	1.6320e+07
rg_reciprocal	37.92 Å
i0_reciprocal	1150000000.0000
total_estimate	0.8835
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	46.2 Å
skewness	0.252
kurtosis	-0.365
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0001
highest_alpha	494600000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.873; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.884

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4. Crystallography & Experiment

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5. Entities & Polymer Info (11)

Entity 1 polymer

description	Methyl-coenzyme M reductase subunit alpha
formula_weight	61535.5 kDa
ec_number	2.8.4.1
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,D
atom_count	43033

MAVRFQKAMETKYTKEWGSNKNKGGKITDKKAKYLRLGYQQNPRKVEMAKCGAAITKKRGLQAYDPKLHLAGIPMGQRQLTPYTISGTDIVCDGDDLHFVNNAAMQQEWDDIRRSCVVGLDLAHEVLEKRLGKEVTPETINYYLEVLNHAMPGAAIVQEHMVETHPALVDDCYVKIFTGDETLQDEVDKQFVINIDNEFPANQAKQIKAAVGKTSWQAVHIPTIVTRTEDGPGTSRWMAMQVGMTFISAYHMCAGEAAVGELAFTAKHAGLVEMGDMIPARRARGPNEPGGLSFGHMADICQTNRKGPEDPVNVILQTASAATMLYDQIWLGGYMSGGVGFTMYATPAYTNDIVDDFLYWADEYASKKYGGRGKAKATIDTVKDIATESTLYSLEAYEKYPTTLEDHFGGSQRATVCSIAAGGATALATGHSQAGLSAWYLSMYLHKEAHGRLGFFGYDLQDQCGATNVFSIASDEGCIGECRGANYPNYAMNVGHQGGYTSVVAAAHAGKDAFCVNPLVKVCFADELINFDFADPRGAFGKAALREWDRCAGERAFVIPAK

Entity 2 polymer

description	Methyl-coenzyme M reductase subunit beta
formula_weight	45366.7 kDa
ec_number	2.8.4.1
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,E

MADTIDLYSDRGAKLKSGVDINDISPMRNAAIKSIVTGIKRTAAVDLAGIEKTLATSAIGGKGRKIPGREMKLDIVKNAAAIQKAVTEMVQVDSGDDTVVKALNGGKQLIVQVPSVRIDVAAEYVSSLTCTASAVTQALVSQFNIGMFDAPTVKSAVWGQYPQTLDMVGGNVKSIVEIPQKDEGFGYTLRNVMANHLAAVCKKNAMNTAALCSILENTGVFEMGDAIGNQTRHRLLAFSHQGLNANNMVYGTTKALGKTGTIGSAVHACVEKAIADKVISADKKFASGYTTYKTNDVGKWNAYCAAGTLVATLINCGAQRAPQAVSSVLLYFQDLIEKETSLPGCDFGKVQGAAVGFSFFSHSIYGGGGPGVFNGNHVVTRHSKGLAVPCVAAAVALDAGVQVYSPEKTSGLVGDVFSAVDEFREPIKAVAGAV

Entity 3 polymer

description	coenzyme-B sulfoethylthiotransferase
formula_weight	28197.8 kDa
ec_number	2.8.4.1
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,F

MAYKPQYYPGSTSVAKNRRKFMSDDVEKMRDISDEDLTALLGHRAPGSDYPSTHPPLSEIGEPACPVREVVEPTPGAAAGDRMRYVQFADSMYNGPAVPYWRSYHAAINFRGVDPGTLSGRQVNEMRERDMEEYAKRQSETEITDWGLAGMRGCTVHGXSLRLQEDGVMFDMLDRRRLEGGVIVSDKDQVGVPIDRKVNLGKPMSEAEAAKRTTIYRVDNVAFRSDKEVIEHVQRVWELRTKYGFVPKA

Entity 4 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	21

Entity 6 non-polymer

description	NITRATE ION
formula_weight	62.0 kDa
src_method	syn
entity_count	5

Entity 7 non-polymer

description	FACTOR 430
formula_weight	906.6 kDa
src_method	syn
entity_count	2

Entity 8 non-polymer

description	Coenzyme B
formula_weight	343.3 kDa
src_method	syn
entity_count	2

Entity 9 non-polymer

description	1-THIOETHANESULFONIC ACID
formula_weight	142.2 kDa
src_method	nat
entity_count	2

Entity 10 non-polymer

description	POTASSIUM ION
formula_weight	39.1 kDa
src_method	syn
entity_count	2

Entity 11 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	3419

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6. Citations (1)

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length_a	81.575 Å
length_b	189.299 Å
length_c	84.109 Å
angle_alpha	90.00 °
angle_beta	114.27 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	0.980 Å
resolution_low	41.780 Å
r_factor	0.1033
r_work	0.1025
r_free	0.1176

fit	/app/data/saxs_computation/qr/9qr1/9qr1.fit
pddf	/app/data/pr_computation/qr/9qr1/9qr1.pr.out
profile	/app/data/saxs_computation/qr/9qr1/9qr1.dat

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

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction

5. Entities & Polymer Info (11)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 non-polymer

Entity 11 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)