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9qts

Structure of the energy converting methyltransferase (Mtr) of Methanosarcina mazei in complex with a novel protein binder

Method: ELECTRON MICROSCOPY D_max: 182.4 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qts
deposition_date	2025-04-09
title	Structure of the energy converting methyltransferase (Mtr) of Methanosarcina mazei in complex with a novel protein binder
keywords	;Sodium-pumping, membrane-bound, methyltransferase complex, methanogen, methanogenic, methylotrophic, archaeon, archaea, methanosarcina, methanosarcina mazei, Vitamin B12, corrinoid, cobalt, 5-hydroxybenzimidazole, small protein, oxygen-sensitive, MEMBRANE PROTEIN ;; MEMBRANE PROTEIN
method	ELECTRON MICROSCOPY

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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	58.36 Å
rg_electron	57.98 Å
i0	8859410000.00
molecular_weight	547080.0 kDa
excluded_volume	542300 Å³
envelope_volume	951310 Å³
shell_volume	131390 Å³
envelope_diameter	188.9 Å
shell_rg	63.88 Å
envelope_rg	57.18 Å
shape_rg	57.68 Å
total_rg	58.63 Å
total_atoms	42783
n_residues	5432
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	182.4 Å
rg_real	58.10 Å
rg_real_error	1.47 Å
i0_real	8.8590e+09
i0_real_error	1.9380e+08
rg_reciprocal	58.55 Å
i0_reciprocal	8865000000.0000
total_estimate	0.6380
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	74.3 Å
skewness	0.129
kurtosis	-0.542
angular_range	— – 0.1350 Å⁻¹
current_alpha	0.0000
highest_alpha	223800000.0000
n_real_points	28
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.945; Stabil: 1.000; Sysdev: 0.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.473

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4. Crystallography & Experiment

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5. Entities & Polymer Info (16)

Entity 1 polymer

description	Tetrahydromethanopterin S-methyltransferase subunit A
formula_weight	25395.2 kDa
ec_number	7.2.1.4
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	45424

MADKREPAPGWPILKGEYEVGDVKNSVLVITCGSHLPGKPILDAGAACTGSCKTENLGIEKVVAHIISNPNIRYLLVTGSEVKGHITGQSMMSLHANGVKENRIAGALGAIPYVENLNAAAVARFQEQVQVVNLLDTEDMGAITSKVRELASKDPGAFDADPLVVEISEEGEEEEEGGVVRPVSGEIAVLRSRLKAIEARMMDIGNLNKFHSGVHAGKVEGAMIGLTITISLLGLLLLGR

Source

organism	Methanosarcina mazei Go1
common_name	MtrA
ncbi_taxonomy_id	192952
host_organism	Methanosarcina mazei Go1

Entity 2 polymer

description	Tetrahydromethanopterin S-methyltransferase subunit B
formula_weight	11879.6 kDa
ec_number	7.2.1.4
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	D,E,F

MSIVRIAPEINLVMDTESGTVTQERKDSIQYSMEPVFERVDKLDAIADDLVNSLSPSKPLLNTWPGRENTSYIAGIYSNSFYGIIVGLAFSGLLALIIYITRLMGGVV

Source

organism	Methanosarcina mazei Go1
common_name	MtrB
ncbi_taxonomy_id	192952
host_organism	Methanosarcina mazei Go1

Entity 3 polymer

description	Tetrahydromethanopterin S-methyltransferase subunit C
formula_weight	26953.9 kDa
ec_number	7.2.1.4
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	G,H,I

MSAGGAGGEAKGAYPQQTLMALGIVGGLVGIYLGHFMPPAYSFFGGIGAICATVWGADAVRRVASYGLGTGVPSIGMLALGMGILAALFGLALGGIAGPILAVVVAAIIGGVIGALANKVIGMGIPIMEQAMIEISCAGTLVILGLSVVIAGSFDYAAIIENVIANGYIALIFIIGGMGILHPFNACLGPDESQDRTLILAVEKAAIALIITGFASSLHEGLMTAGINILVGLVIWYVAFSKYYALIKRDAYAVVGTGLLPSAEELQ

Source

organism	Methanosarcina mazei Go1
ncbi_taxonomy_id	192952
host_organism	Methanosarcina mazei Go1

Entity 4 polymer

description	Tetrahydromethanopterin S-methyltransferase subunit D
formula_weight	25279.8 kDa
ec_number	7.2.1.4
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	J,K,L

MIDAILGNILWMVFIIIGGVLISWGVHFVPVGGAPAAMAQATGVGTGTVQLATGAGLTGLVSAGFMMNVTDNFPLIVASGAVGAMIMIAVTMIVGTWIYVYGVGCVPSSAKVKVDPITKYRQDLYVSQGTEGHGIPTVSFVSGVIGAALGGIGGSLIYYSLIEVGVSVGLERVGVTSAVTGNSLVAVAAIFAIGIFLVNAVIPSYNIGGTIEGFHDPKFKKWPKAVISSVVASILCAIVAVIAIAQLGGI

Source

organism	Methanosarcina mazei Go1
common_name	MtrD
ncbi_taxonomy_id	192952
host_organism	Methanosarcina mazei Go1

Entity 5 polymer

description	Tetrahydromethanopterin S-methyltransferase subunit E
formula_weight	35539.6 kDa
ec_number	7.2.1.4
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	M,N,O

MEPLIGMGVLALIGVAATIAGASEDLESDIGSQSNPNSQVQLAPQMMFPHRIFNKAISGEPPSNALMCSIGAAIATVLISEFTVSPLFALVFGSVIAASVHATFAVTATMGRCASQSRFKQPIYLDMIRSHTPAIMGYAFITTFCVLIVSYLMTVVLGHPFPLTMLAFIWGITIGAIGSSTGDVHYGAEREFQQFEFGSGLNASNSGNIVRYAESGLRNGFDNSWFCSKFGGPTTGIAFGMTVFLGSWITTIFDPAQGLSMGWLSVIAGVIIVLILIIWNWKIEVQARKAYGPYKEDKAEEASASAWSHPQFEKGGGSGGGSGGSAWSHPQFEK

Source

organism	Methanosarcina mazei Go1
common_name	MtrE
ncbi_taxonomy_id	192952
host_organism	Methanosarcina mazei Go1

Entity 6 polymer

description	Tetrahydromethanopterin S-methyltransferase subunit F
formula_weight	7574.0 kDa
ec_number	7.2.1.4
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	P,Q,R

MAEEHEKGVPMVLAPQMGAIDATVESIRYRAQLIARNQKLDSGVAATGIIGFAAGFLFSLLMVIVLPVAVGL

Source

organism	Methanosarcina mazei Go1
common_name	MtrF
ncbi_taxonomy_id	192952
host_organism	Methanosarcina mazei Go1

Entity 7 polymer

description	Tetrahydromethanopterin S-methyltransferase subunit G
formula_weight	8030.4 kDa
ec_number	7.2.1.4
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	S,T,U

MDGKAPAAFVEPGEFNEVMKRLDQIDEKVEFVNSEVAQRIGKKVGRDIGILYGGVIGLLLFLIYVQISSMFM

Source

organism	Methanosarcina mazei Go1
common_name	MtrG
ncbi_taxonomy_id	192952
host_organism	Methanosarcina mazei Go1

Entity 8 polymer

description	Conserved protein
formula_weight	7623.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	i

MKCEACGRESDTKYCNDCGKVMDEVVRRVGEARWAAIDDCSFIYPLVQRVGRGEATVNDIIQALDVED

Source

organism	Methanosarcina mazei Go1
common_name	MtrI
ncbi_taxonomy_id	192952
host_organism	Methanosarcina mazei Go1

Entity 9 polymer

description	Tetrahydromethanopterin S-methyltransferase subunit H
formula_weight	34075.7 kDa
ec_number	7.2.1.4
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	m,n,o,p,q,r

MFKFDKKQEVFELGGVKFGGQPGENPTVLVSTMFYARHKIVTDEDKGIFDRAAAETLWNTQVSLSDATGLPYVNQIVGETPESIKRYIEWFVGIDDRTPFLIDSSAGNVRAAAAQYCTEIGVADRAIHNSINASIEQSEIDVLTESDVSAAIVLAFNATDPTVKGKIDILEVGGSGQTKGMLQVAKECGIKYPIIDVAAMPLGAGSGATIRSVPTLKGKFGLPIGGGYHNMASAWDWLRKFKKTQPDPKAIYMPTDIGTNLVAQIAGSDYLLYGPIENVNQIFPAVAMVDIMLGETAKELGVEIADLENHPVTKLT

Source

organism	Methanosarcina mazei Go1
common_name	MtrH
ncbi_taxonomy_id	192952
host_organism	Methanosarcina mazei Go1

Entity 10 non-polymer

description	5-HYDROXYBENZIMIDAZOLYLCOB(III)AMIDE
formula_weight	1321.3 kDa
src_method	syn
entity_count	1

Entity 11 non-polymer

description	2-Hydroxy-archaetidylinositol
formula_weight	836.2 kDa
src_method	syn
entity_count	6

Entity 12 non-polymer

description	3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL
formula_weight	733.1 kDa
src_method	nat
entity_count	3

Entity 13 non-polymer

description	Archaetidylinositol
formula_weight	911.3 kDa
src_method	syn
entity_count	3

Entity 14 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	3

Entity 15 non-polymer

description	Archaetidylethanolamine
formula_weight	776.2 kDa
src_method	syn
entity_count	3

Entity 16 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	2641

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.10 Å
resolution_method	—
num_particles	150000

fit	/app/data/saxs_computation/qt/9qts/9qts.fit
pddf	/app/data/pr_computation/qt/9qts/9qts.pr.out
profile	/app/data/saxs_computation/qt/9qts/9qts.dat

Structure of the energy converting methyltransferase (Mtr) of Methanosarcina mazei in complex with a novel protein binder

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

EM 3D

5. Entities & Polymer Info (16)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

Entity 6 polymer

Polymer

Source

Entity 7 polymer

Polymer

Source

Entity 8 polymer

Polymer

Source

Entity 9 polymer

Polymer

Source

Entity 10 non-polymer

Entity 11 non-polymer

Entity 12 non-polymer

Entity 13 non-polymer

Entity 14 non-polymer

Entity 15 non-polymer

Entity 16 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)