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9pym

Cryo-EM structure of the isethionate TRAP transporter IseQM from Oleidesulfovibrio alaskensis with bound isethionate

Method: ELECTRON MICROSCOPY D_max: 88.4 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9pym
deposition_date	2025-08-07
title	Cryo-EM structure of the isethionate TRAP transporter IseQM from Oleidesulfovibrio alaskensis with bound isethionate
keywords	TRAP Transporter, Megabody, Isethionate, TRANSPORT PROTEIN; TRANSPORT 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	28.08 Å
rg_electron	26.79 Å
i0	80903100.00
molecular_weight	78450.0 kDa
excluded_volume	101520 Å³
envelope_volume	118840 Å³
shell_volume	36342 Å³
envelope_diameter	92.7 Å
shell_rg	34.61 Å
envelope_rg	26.96 Å
shape_rg	26.80 Å
total_rg	27.61 Å
total_atoms	11259
n_residues	717
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	88.4 Å
rg_real	27.95 Å
rg_real_error	0.53 Å
i0_real	8.0900e+07
i0_real_error	1.1600e+06
rg_reciprocal	27.99 Å
i0_reciprocal	80910000.0000
total_estimate	0.9009
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	34.7 Å
skewness	0.221
kurtosis	-0.403
angular_range	— – 0.2800 Å⁻¹
current_alpha	0.0000
highest_alpha	12590000.0000
n_real_points	57
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.912; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.974

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Isethionate TRAP transporter permease protein DctMQ
formula_weight	67592.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	11259

MSDPNVTATIMNAQGECSSGSLESRPGILGWLDANFEKPFLVAGMLAIIFIITFQTLYRYIGVYLHEGAAAAVWTEEMARFIFIWISYLAVPVAIKNRSSIRVDIIFDRLPVRFQNISWIIVDVCFLTLAATVLWQSLDLIKMQLTYPQTSPALQLPYYIPYLVLPVSFGLMAVRLLQDLAGQVRICGAADTVIGLILCAVLAAPLFIADYIDPLPVLFGYFALFLVVGVPIAIGLGLAALATIVAAGSLPIDYVAQIAFTSIDSFPIMAIPFFIAAGVFMGAGGLSRRLLNLADEMLGALPGGMALATIGTCMFFAAISGSGPATVAAIGSLTIPAMVERGYCKYFSAAIVAAAGAIGVMIPPSNPFVVYGVSAQASIGKLFMGGIVPGLLTGLALMAYSYWYSKKRGWKGEVRDRNLKTFMHAVWEAKWALMVPVIVLGGIYGGIMTPTEAAALAAFYGLIIGCFVHRELSCGSFYDCVVEAAGTSAMVIVLMSMATIFGNIMTIEEVPTTIAQAMLGLTTDKIAILLMINVLLLIIGTFMEALAAIVILTPILLPIVLKVGVDPVHFGIIMVVNLAIGFVTPPVGVNLFVASGVANAKIEQLSKVVLPLIALMLAVLLITTYVPAIPMFFAG

Source

organism	Oleidesulfovibrio alaskensis G20
ncbi_taxonomy_id	207559
host_organism	Escherichia coli

Entity 2 polymer

description	Megabody C7HopQ
formula_weight	55463.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

QVSLQESGGGLVQTKTTTSVIDTTNDAQNLLTQAQTIVNTLKDYCPILIAKSSSSNGGTNNANTPSWQTAGGGKNSCATFGAEFSAASDMINNAQKIVQETQQLSANQPKNITQPHNLNLNSPSSLTALAQKMLKNAQSQAEILKLANQVESDFNKLSSGHLKDYIGKCDASAISSANMTMQNQKNNWGNGCAGVEETQSLLKTSAADFNNQTPQINQAQNLANTLIQELGNNTYEQLSRLLTNDNGTNSKTSAQAINQAVNNLNERAKTLAGGTTNSPAYQATLLALRSVLGLWNSMGYAVICGGYTKSPGENNQKDFHYTDENGNGTTINCGGSTNSNGTHSYNGTNTLKADKNVSLSIEQYEKIHEAYQILSKALKQAGLAPLNSKGEKLEAHVTTSKYAGGSLRLSCAASGNIFLWANMGWYRQAPGKEREFVASISLGANTNYADSVKGRFTISRDNAKNTVYLQMNSLKQEDTAVYYCAVWARYPSTYYLGRGYDYLYWGQGTQVTVSS

Source

organism	Helicobacter pylori
ncbi_taxonomy_id	210
host_organism	Escherichia coli

Entity 3 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	2-hydroxyethylsulfonic acid
formula_weight	126.1 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	PHOSPHATIDYLETHANOLAMINE
formula_weight	734.0 kDa
src_method	syn
entity_count	3

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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	2.98 Å
resolution_method	—
num_particles	83854

fit	/app/data/saxs_computation/py/9pym/9pym.fit
pddf	/app/data/pr_computation/py/9pym/9pym.pr.out
profile	/app/data/saxs_computation/py/9pym/9pym.dat

Cryo-EM structure of the isethionate TRAP transporter IseQM from Oleidesulfovibrio alaskensis with bound isethionate

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 (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)