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9qtp

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

Method: ELECTRON MICROSCOPY D_max: 89.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qtp
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	26.97 Å
rg_electron	25.81 Å
i0	81370100.00
molecular_weight	72241.0 kDa
excluded_volume	91021 Å³
envelope_volume	106150 Å³
shell_volume	33883 Å³
envelope_diameter	91.4 Å
shell_rg	33.94 Å
envelope_rg	26.16 Å
shape_rg	25.81 Å
total_rg	26.62 Å
total_atoms	5082
n_residues	670
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	89.6 Å
rg_real	26.96 Å
rg_real_error	0.63 Å
i0_real	8.1370e+07
i0_real_error	1.1190e+06
rg_reciprocal	26.96 Å
i0_reciprocal	81370000.0000
total_estimate	0.8721
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	31.9 Å
skewness	0.408
kurtosis	-0.191
angular_range	— – 0.2950 Å⁻¹
current_alpha	0.0000
highest_alpha	22860000.0000
n_real_points	60
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.811; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.913

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Tetrahydromethanopterin S-methyltransferase subunit B
formula_weight	11879.6 kDa
ec_number	7.2.1.4
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E
atom_count	5082

MSIVRIAPEINLVMDTESGTVTQERKDSIQYSMEPVFERVDKLDAIADDLVNSLSPSKPLLNTWPGRENTSYIAGIYSNSFYGIIVGLAFSGLLALIIYITRLMGGVV

Entity 2 polymer

description	Tetrahydromethanopterin S-methyltransferase subunit F
formula_weight	7574.0 kDa
ec_number	7.2.1.4
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	P

MAEEHEKGVPMVLAPQMGAIDATVESIRYRAQLIARNQKLDSGVAATGIIGFAAGFLFSLLMVIVLPVAVGL

Entity 3 polymer

description	Tetrahydromethanopterin S-methyltransferase subunit H
formula_weight	34075.7 kDa
ec_number	7.2.1.4
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	o,p

MFKFDKKQEVFELGGVKFGGQPGENPTVLVSTMFYARHKIVTDEDKGIFDRAAAETLWNTQVSLSDATGLPYVNQIVGETPESIKRYIEWFVGIDDRTPFLIDSSAGNVRAAAAQYCTEIGVADRAIHNSINASIEQSEIDVLTESDVSAAIVLAFNATDPTVKGKIDILEVGGSGQTKGMLQVAKECGIKYPIIDVAAMPLGAGSGATIRSVPTLKGKFGLPIGGGYHNMASAWDWLRKFKKTQPDPKAIYMPTDIGTNLVAQIAGSDYLLYGPIENVNQIFPAVAMVDIMLGETAKELGVEIADLENHPVTKLT

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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	triclinic

resolution	3.20 Å
resolution_method	—
num_particles	136531

fit	/app/data/saxs_computation/qt/9qtp/9qtp.fit
pddf	/app/data/pr_computation/qt/9qtp/9qtp.pr.out
profile	/app/data/saxs_computation/qt/9qtp/9qtp.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 (3)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)