← Back to search

9qqt

Methyl-coenzyme M reductase of ANME-2d Candidatus Methanoperedens Vercelli Strain 1 from a bioreactor enrichment culture

Method: X-RAY DIFFRACTION D_max: 121.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9qqt
deposition_date	2025-04-02
title	Methyl-coenzyme M reductase of ANME-2d Candidatus Methanoperedens Vercelli Strain 1 from a bioreactor enrichment culture
keywords	;methanotrophy, anaerobic methanotrophic archaea, methane oxidation, methyl-coenzyme M reductase, ANME, MCR, reverse methanogenesis, nickel-dependent enzyme, coenzyme M, coenzyme B, F430 cofactor, post-translational modification, TRANSFERASE ;; TRANSFERASE
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	38.02 Å
rg_electron	37.40 Å
i0	1146990000.00
molecular_weight	273240.0 kDa
excluded_volume	339220 Å³
envelope_volume	383150 Å³
shell_volume	79031 Å³
envelope_diameter	128.5 Å
shell_rg	47.34 Å
envelope_rg	37.63 Å
shape_rg	37.52 Å
total_rg	37.48 Å
total_atoms	37826
n_residues	2474
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

▼

3. P(r) Analysis (GNOM)

dmax	121.1 Å
rg_real	37.84 Å
rg_real_error	0.53 Å
i0_real	1.1470e+09
i0_real_error	1.7230e+07
rg_reciprocal	37.95 Å
i0_reciprocal	1147000000.0000
total_estimate	0.8833
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	46.1 Å
skewness	0.256
kurtosis	-0.367
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0001
highest_alpha	500800000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.877; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.870

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (11)

Entity 1 polymer

description	Methyl-coenzyme M reductase subunit alpha
formula_weight	61873.8 kDa
ec_number	2.8.4.1
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	43046

MAEPRFKKSMETKYAKEWGSNKVGSTAKAKITDKKTKYLRLGYQQNPRKVEMAKCGAAITKKRGLQAYDPKLHLAGIPMGQRQLTPYTISGTDIVCDGDDLHFVNNAAMQQEWDDIRRTCVVGLDLAHETLEKRLGKEVTPETINYYLEVLNHAMPGAAIVQEHMVETHPALVDDCYVKIFTGDETLQDEVDKQFVINIDNEFPANQAKQIKAAVGKTSWQAVHIPTIVTRTEDGPGTSRWMAMQVGMTFISAYHMCAGEAAVGELAFTAKHAGLVEMGDMIPARRARGPNEPGGLSFGHMADIVQTNRKGPEDPVNVVLQTASAATMLYDQIWLGGYMSGGVGFTMYATPAYTNDIVDDFLYWGNDYAAKKYGGNGKAKATIDTVKDIATETTLYGLEAYEKYPTTLEDHFGGSQRATVISIAAGGATALATGHSQAGLSAWYLSMYLHKEAHGRLGFYGYDLQDQCGATNVFSIASDEGCIGECRGANYPNYAMNVGHQGGYTSVVAAAHAGKDAFCVNPLVKTCFADELINFDFADPRAAFGKAALREWDRCAGERAFVIPAK

Entity 2 polymer

description	Methyl-coenzyme M reductase subunit beta
formula_weight	45334.6 kDa
ec_number	2.8.4.1
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,E

MADTIDLYSDRGAKLKSGVDINDISPMRNAAIKSIVTGIKRTAAVDLAGIEKTLATSAIGGKGRKIPGREMKLDIVKNAAAIQKAVNELVQVDSGDDTVVKALNGGKQLIVQVPSVRIDVAAEYVSSLTCTASAVTQALVSQFNIGMFDAPTIKSAVWGQYPQTLDMVGGNVKSIVDIPQKDEGFGYTLRNVMANHLAATCKKSAMNTAALCSILENTGVFEMGDAIGNQTRHRLLAFSHQGLNANNLVYGTTKALGKTGTIGSAVHACVEKAIADKVISADKKFASGYTTYKTNDVGKWNAYCAAGTLVATLINCGAQRAPQSVSAVLLYFNDLIEKETSLPGCDFGKVQGAAVGFSFFSHSIYGGGGPGVFNGNHVVTRHSKGLAVPCVAAAVALDAGVQIYSPEKTSGLVGDVFSSVDEFREPIKAVAGAV

Entity 3 polymer

description	Methyl-coenzyme M reductase subunit gamma
formula_weight	28253.8 kDa
ec_number	2.8.4.1
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,F

MAYKPQYYPGSTSVAKNRRKHMSDDVEKMRDISDEDLTALLGHRAPGSDYPSTHPPLSEIGEPACSVREVVEPTPGAAAGDRLRYVQWSDSMYNAPSVPYWRSYHAAINFRGVDPGTLSGRQVNEMRERDMEEYAKRQAETEMTDWGLAGMRGCTVHGXSLRLQEDGVMFDMLDRRRLEGGVIVSDKDQVGVPIDRKVNLGKPMSEAEAAKRTTFYRVDNVAFRSDKEVIEHVQKVWELRTKYGFVPKA

Entity 4 polymer

description	Methyl-coenzyme M reductase subunit alpha
formula_weight	61857.8 kDa
ec_number	2.8.4.1
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

Entity 5 non-polymer

description	POTASSIUM ION
formula_weight	39.1 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	FACTOR 430
formula_weight	906.6 kDa
src_method	nat
entity_count	2

Entity 7 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	22

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	syn
entity_count	2

Entity 10 non-polymer

description	O-PHOSPHONO-N-{(2E)-7-[(2-SULFOETHYL)DITHIO]HEPT-2-ENOYL}-L-THREONINE
formula_weight	481.5 kDa
src_method	nat
entity_count	2

Entity 11 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	3293

▶

6. Citations (1)

▶

length_a	81.621 Å
length_b	189.823 Å
length_c	83.930 Å
angle_alpha	90.00 °
angle_beta	114.36 °
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	41.710 Å
r_factor	0.1293
r_work	0.1283
r_free	0.1481

fit	/app/data/saxs_computation/qq/9qqt/9qqt.fit
pddf	/app/data/pr_computation/qq/9qqt/9qqt.pr.out
profile	/app/data/saxs_computation/qq/9qqt/9qqt.dat

Methyl-coenzyme M reductase of ANME-2d Candidatus Methanoperedens Vercelli Strain 1 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 polymer

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)