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10ky

X-ray structure of the Bacteroides fragilis Nramp/MntH divalent transition metal transporter WT in an inward-open, state

Method: X-RAY DIFFRACTION D_max: 92.2 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	10ky
deposition_date	2026-01-26
last_revision	2026-03-04
title	X-ray structure of the Bacteroides fragilis Nramp/MntH divalent transition metal transporter WT in an inward-open, state
keywords	Membrane Protein, Divalent metal transporter, Manganese Homeostasis, Iron Homeostasis, METAL TRANSPORT; METAL TRANSPORT
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	28.59 Å
rg_electron	28.34 Å
i0	82246200.00
molecular_weight	91661.0 kDa
excluded_volume	123590 Å³
envelope_volume	140350 Å³
shell_volume	40051 Å³
envelope_diameter	95.8 Å
shell_rg	36.62 Å
envelope_rg	28.75 Å
shape_rg	28.34 Å
total_rg	29.34 Å
total_atoms	6465
n_residues	749
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	92.2 Å
rg_real	28.53 Å
rg_real_error	0.53 Å
i0_real	8.2250e+07
i0_real_error	1.1040e+06
rg_reciprocal	28.55 Å
i0_reciprocal	82250000.0000
total_estimate	0.9001
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	33.5 Å
skewness	0.254
kurtosis	-0.456
angular_range	— – 0.2750 Å⁻¹
current_alpha	0.0000
highest_alpha	22100000.0000
n_real_points	56
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.966

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Divalent metal cation transporter
formula_weight	45392.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	6507

MHHHHHHHHAHMKRYLGGLDVFRYIGPGLLVTVGFIDPGNWASNFAAGSEFGYSLLWVVTLSTIMLIILQHNVAHLGIVTGLCLSEAATQYTPKWVSRPILGTAVLASISTSLAEILGGAIALEMLLDIPIVWGAVLTTVFVSIMLFTNSYKKIERSIIAFVSVIGLSFIYELFLVDIDWPMAVEGWVTPAIPKGSMLIIMSVLGAVVMPHNLFLHSEVIQSHEYNKQDTASIKKVLKYELFDTLFSMIIGWAINSAMILLAAATFFKSGIQVEELQQAKSLLEPLLGSNAAIVFALALLMAGISSTITSGMAAGSIFAGIFGESYHIKDSHSQVGVILSLGIALLLIFFIGDPFKGLIISQMVLSIQLPFTVFLQVGLTSSRKVMGDYVNSKWSTFVLYTIAVIVTVLNIMLLFS

Source

organism	Bacteroides fragilis
ncbi_taxonomy_id	817
host_organism	Escherichia coli

Entity 2 non-polymer

description	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
formula_weight	356.5 kDa
src_method	syn
entity_count	47

Entity 3 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	3

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	42

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6. Citations (1)

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length_a	69.119 Å
length_b	102.272 Å
length_c	119.220 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 2 21
int_tables_number	18
crystal_system	orthorhombic

resolution	2.480 Å
resolution_low	45.140 Å
r_factor	0.2615
r_work	0.2590
r_free	0.2985

fit	/app/data/saxs_computation/0k/10ky/10ky.fit
pddf	/app/data/pr_computation/0k/10ky/10ky.pr.out
profile	/app/data/saxs_computation/0k/10ky/10ky.dat

X-ray structure of the Bacteroides fragilis Nramp/MntH divalent transition metal transporter WT in an inward-open, state

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