Crystal structure of Leminorella grimontii GatC in the absence of D-xylose

Method: X-RAY DIFFRACTION D_max: 98.1 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9u8h
deposition_date	2025-03-26
title	Crystal structure of Leminorella grimontii GatC in the absence of D-xylose
keywords	PTS, transporter, xylose, TRANSPORT PROTEIN; TRANSPORT PROTEIN
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	31.16 Å
rg_electron	30.55 Å
i0	116905000.00
molecular_weight	96677.0 kDa
excluded_volume	125860 Å³
envelope_volume	152860 Å³
shell_volume	40765 Å³
envelope_diameter	103.5 Å
shell_rg	38.54 Å
envelope_rg	30.47 Å
shape_rg	30.54 Å
total_rg	31.39 Å
total_atoms	6812
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	98.1 Å
rg_real	31.08 Å
rg_real_error	0.65 Å
i0_real	1.1690e+08
i0_real_error	1.7060e+06
rg_reciprocal	31.12 Å
i0_reciprocal	116900000.0000
total_estimate	0.9070
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	36.5 Å
skewness	0.227
kurtosis	-0.558
angular_range	— – 0.2550 Å⁻¹
current_alpha	0.0000
highest_alpha	19850000.0000
n_real_points	52
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.943; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.958

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

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6. Citations (1)

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length_a	87.870 Å
length_b	100.840 Å
length_c	122.880 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 2 21 21
int_tables_number	18
crystal_system	—

resolution	3.740 Å
resolution_low	46.650 Å
r_factor	0.2568
r_work	0.2536
r_free	0.2855

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

type	polypeptide(L)
strand_id	A,B
atom_count	6812

Crystal structure of Leminorella grimontii GatC in the absence 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

Diffraction

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Leminorella grimontii
ncbi_taxonomy_id	82981
host_organism	Escherichia coli

description	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
formula_weight	356.5 kDa
src_method	syn
entity_count	6

fit	/app/data/saxs_computation/u8/9u8h/9u8h.fit
pddf	/app/data/pr_computation/u8/9u8h/9u8h.pr.out
profile	/app/data/saxs_computation/u8/9u8h/9u8h.dat