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10lg

Crystal structure of Streptococcus thermophilus SHP pheromone receptor Rgg3 in complex with Rgg3bp13

Method: X-RAY DIFFRACTION D_max: 83.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	10lg
deposition_date	2026-01-26
last_revision	2026-02-04
title	Crystal structure of Streptococcus thermophilus SHP pheromone receptor Rgg3 in complex with Rgg3bp13
keywords	DNA Binding Protein, RRNPP Protein, Quorum Sensing, Peptide Inhibitor; DNA BINDING 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	23.92 Å
rg_electron	22.94 Å
i0	20051000.00
molecular_weight	34346.0 kDa
excluded_volume	43119 Å³
envelope_volume	53233 Å³
shell_volume	20761 Å³
envelope_diameter	85.0 Å
shell_rg	28.18 Å
envelope_rg	23.31 Å
shape_rg	22.91 Å
total_rg	23.72 Å
total_atoms	4795
n_residues	286
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	83.2 Å
rg_real	24.08 Å
rg_real_error	0.68 Å
i0_real	2.0050e+07
i0_real_error	2.9900e+05
rg_reciprocal	24.04 Å
i0_reciprocal	20050000.0000
total_estimate	0.8405
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.4 Å
skewness	0.500
kurtosis	-0.258
angular_range	— – 0.3300 Å⁻¹
current_alpha	0.0000
highest_alpha	4766000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.755; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.803; Smooth: 0.854

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Positive transcriptional regulator MutR family
formula_weight	33242.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4931

MKSKLGSTLRKVRNGKQISICSVADEHLSKSQISRFERGESEISCIRLINILDKLHITLDEFLILHDEDYTKTESFANLVQYIRKQYSLQNINNIQSLLSDSSNYTLDPFEKTMVKSILHTMDSSIIPSDDELLQLADYLFKVEKWGYYEIILLGNCVRTIDYNSVFLLTKEMLNNYIYSSLNKTNKRIVTQLAINCLILSIDMEEFTNCFYLIDEIKALLDNELNFYEQTVFLYATGYFEFKRWQSTSGIEKMKQAIQVLDILGEDNLKLHYTIHFDKLINNK

Source

organism	Streptococcus thermophilus LMG 18311
ncbi_taxonomy_id	264199
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	Rgg3bp13 peptide
formula_weight	2127.5 kDa
src_method	syn
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

SLTDDLWRAMMEAWMRL

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	5

Entity 4 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
formula_weight	122.1 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	122

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6. Citations (1)

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length_a	111.678 Å
length_b	111.678 Å
length_c	50.749 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 32 2 1
int_tables_number	154
crystal_system	trigonal

resolution	1.870 Å
resolution_low	19.940 Å
r_factor	0.1865
r_work	0.1830
r_free	0.2177

fit	/app/data/saxs_computation/0l/10lg/10lg.fit
pddf	/app/data/pr_computation/0l/10lg/10lg.pr.out
profile	/app/data/saxs_computation/0l/10lg/10lg.dat

Crystal structure of Streptococcus thermophilus SHP pheromone receptor Rgg3 in complex with Rgg3bp13

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 (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)