Cryo-EM structure of Leminorella grimontii GatC in the presence of D-xylose

Method: ELECTRON MICROSCOPY D_max: 97.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9u82
deposition_date	2025-03-25
title	Cryo-EM structure of Leminorella grimontii GatC in the presence of D-xylose
keywords	PTS, D-xylose, transporter, 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	30.61 Å
rg_electron	29.77 Å
i0	117319000.00
molecular_weight	95214.0 kDa
excluded_volume	123290 Å³
envelope_volume	144970 Å³
shell_volume	39495 Å³
envelope_diameter	98.8 Å
shell_rg	38.01 Å
envelope_rg	29.78 Å
shape_rg	29.76 Å
total_rg	30.59 Å
total_atoms	6708
n_residues	896
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	97.3 Å
rg_real	30.53 Å
rg_real_error	0.59 Å
i0_real	1.1730e+08
i0_real_error	1.4970e+06
rg_reciprocal	30.56 Å
i0_reciprocal	117300000.0000
total_estimate	0.8310
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	35.5 Å
skewness	0.225
kurtosis	-0.574
angular_range	— – 0.2600 Å⁻¹
current_alpha	0.0000
highest_alpha	20200000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (1)

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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	2.700 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.70 Å
resolution_method	—
num_particles	442864

description	PTS galactitol transporter subunit IIC
formula_weight	50078.1 kDa
src_method	man
entity_count	2

Cryo-EM structure of Leminorella grimontii GatC in the presence of D-xylose

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

EM 3D

5. Entities & Polymer Info (1)

Entity 1 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Leminorella grimontii
ncbi_taxonomy_id	82981
host_organism	Escherichia coli

fit	/app/data/saxs_computation/u8/9u82/9u82.fit
pddf	/app/data/pr_computation/u8/9u82/9u82.pr.out
profile	/app/data/saxs_computation/u8/9u82/9u82.dat

type	polypeptide(L)
strand_id	A,B
atom_count	6708