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6w1e

Crystal structure of Streptococcus thermophilus SHP pheromone receptor Rgg3

Method: X-RAY DIFFRACTION Dmax: 56.7 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Positive transcriptional regulator MutR family

Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311)

UniProt Q5M4D0

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–284 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

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 6W1E Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
10LG Crystal structure of Streptococcus thermophilus SHP pheromone receptor Rgg3 in complex with Rgg3bp13 Deposited 2026-01-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–284（284 aa）
Not recorded 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
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.

SAXS scattering curve SAXS Profile

SAXS profile for 6w1e

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6w1e
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6w1e
Deposition date deposition_date2020-03-04
Structure title titleCrystal structure of Streptococcus thermophilus SHP pheromone receptor Rgg3
Keywords keywordsPHEROMONE BINDING, QUORUM SENSING, DNA BINDING PROTEIN, RRNPP; DNA BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier18.76 Å
Radius of gyration Rg (electron density) rg_electron17.55 Å
Forward intensity I(0) i09749880.00
Molecular weight molecular_weight24006.0 kDa
Excluded volume excluded_volume30452 ų
Envelope volume envelope_volume35883 ų
Hydration-shell volume shell_volume17143 ų
Envelope diameter envelope_diameter57.1 Å
Shell Rg shell_rg23.57 Å
Envelope Rg envelope_rg17.55 Å
Shape Rg shape_rg17.54 Å
Total Rg total_rg18.59 Å
Total atoms total_atoms1688
Residues n_residues202
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax56.7 Å
Rg (real space) rg_real18.62 Å
Rg uncertainty (real space) rg_real_error0.25 Å
I(0) (real space) i0_real9.7500e+06
I(0) uncertainty (real space) i0_real_error1.1410e+05
Rg (reciprocal space) rg_reciprocal18.64 Å
I(0) (reciprocal space) i0_reciprocal9750000.0000
Solution quality estimate total_estimate0.7467
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.4 Å
Skewness Skewness skewness0.038
Kurtosis Kurtosis kurtosis-0.544
Angular range angular_range— – 0.4250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1910000.0000
Real-space data points n_real_points74
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.938; Stabil: 1.000; Sysdev: 0.313; Positv: 1.000; Valcen: 0.986; Smooth: 0.966
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)