SAXSdb — 10lg

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Positive transcriptional regulator MutR family

Streptococcus thermophilus LMG 18311

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–284	Not recorded	Rgg3bp13 peptide × 1 SO4 SULFATE ION × 5 GOL GLYCEROL × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；100 mM sodium citrate pH 5.2, 300 mM Na/K tartrate, and 1.4 M ammonium sulfate	Resolution 1.87 Å R-free 0.218

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 10LG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6W1E Crystal structure of Streptococcus thermophilus SHP pheromone receptor Rgg3 Deposited 2020-03-04	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–284（284 aa）	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.2；298 K；100 mM sodium citrate, 300 mM Na/K tartrate, and 1.4 M ammonium sulfate	Resolution 2.20 Å R-free 0.309
6W1F Crystal structure of Streptococcus thermophilus SHP pheromone receptor Rgg3 bound to DNA Deposited 2020-03-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–284（284 aa） Chain B 1–284（284 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；298 K；170 mM ammonium acetate, 85 mM sodium citrate, 22% PEG 4,000, and 15% glycerol	Resolution 3.20 Å R-free 0.266
7JI0 CryoEM structure of Streptococcus thermophilus SHP pheromone receptor Rgg3 in complex with SHP3 Deposited 2020-07-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–284（284 aa） Chain B 1–284（284 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；2.5 microliters Rgg3St-SHP3 was applied to glow-discharged UltraAuFoil (1.2/1.3) 300-mesh grids (Quantifoil), blotted with filter paper for 3-3.5 s, and flash-frozen by plunging in liquid ethane cooled with liquid nitrogen. Grids were stored in liquid nitrogen.	Resolution 2.95 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q5M4D0_STRT2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–284； UniProt 1–284

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	10lg
Deposition date deposition_date	2026-01-26
最后修订 last_revision	2026-02-04
Structure title title	Crystal structure of Streptococcus thermophilus SHP pheromone receptor Rgg3 in complex with Rgg3bp13
Keywords keywords	DNA Binding Protein, RRNPP Protein, Quorum Sensing, Peptide Inhibitor; DNA BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	23.92 Å
Radius of gyration Rg (electron density) rg_electron	22.94 Å
Forward intensity I(0) i0	20051000.00
Molecular weight molecular_weight	34346.0 kDa
Excluded volume excluded_volume	43119 Å³
Envelope volume envelope_volume	53233 Å³
Hydration-shell volume shell_volume	20761 Å³
Envelope diameter envelope_diameter	85.0 Å
Shell Rg shell_rg	28.18 Å
Envelope Rg envelope_rg	23.31 Å
Shape Rg shape_rg	22.91 Å
Total Rg total_rg	23.72 Å
Total atoms total_atoms	4795
Residues n_residues	286
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	83.2 Å
Rg (real space) rg_real	24.08 Å
Rg uncertainty (real space) rg_real_error	0.68 Å
I(0) (real space) i0_real	2.0050e+07
I(0) uncertainty (real space) i0_real_error	2.9900e+05
Rg (reciprocal space) rg_reciprocal	24.04 Å
I(0) (reciprocal space) i0_reciprocal	20050000.0000
Solution quality estimate total_estimate	0.8405
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.4 Å
Skewness Skewness skewness	0.500
Kurtosis Kurtosis kurtosis	-0.258
Angular range angular_range	— – 0.3300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4766000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria 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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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Positive transcriptional regulator MutR family
Molecular weight formula_weight	33242.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4931

MKSKLGSTLRKVRNGKQISICSVADEHLSKSQISRFERGESEISCIRLINILDKLHITLDEFLILHDEDYTKTESFANLVQYIRKQYSLQNINNIQSLLSDSSNYTLDPFEKTMVKSILHTMDSSIIPSDDELLQLADYLFKVEKWGYYEIILLGNCVRTIDYNSVFLLTKEMLNNYIYSSLNKTNKRIVTQLAINCLILSIDMEEFTNCFYLIDEIKALLDNELNFYEQTVFLYATGYFEFKRWQSTSGIEKMKQAIQVLDILGEDNLKLHYTIHFDKLINNK

来源 Source

来源生物 organism	Streptococcus thermophilus LMG 18311
NCBI Class编号 ncbi_taxonomy_id	264199
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Rgg3bp13 peptide
Molecular weight formula_weight	2127.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SLTDDLWRAMMEAWMRL

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	122

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8. Citations (1)

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Unit-cell length a length_a	111.678 Å
Unit-cell length b length_b	111.678 Å
Unit-cell length c length_c	50.749 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	trigonal

Resolution resolution	1.870 Å
Low-resolution limit resolution_low	19.940 Å
R factor r_factor	0.1865
R_work r_work	0.1830
R_free 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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Positive transcriptional regulator MutR family

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)