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- PDB-10lg: Crystal structure of Streptococcus thermophilus SHP pheromone rec... -

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Basic information

Entry
Database: PDB / ID: 10lg
TitleCrystal structure of Streptococcus thermophilus SHP pheromone receptor Rgg3 in complex with Rgg3bp13
Components
  • Positive transcriptional regulator MutR family
  • Rgg3bp13 peptide
KeywordsDNA BINDING PROTEIN / RRNPP Protein / Quorum Sensing / Peptide Inhibitor
Function / homologyTranscription activator MutR, C-terminal / HTH-type transcriptional regulator Rgg, C-terminal domain / : / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / Tetratricopeptide-like helical domain superfamily / DNA binding / Positive transcriptional regulator MutR family
Function and homology information
Biological speciesStreptococcus thermophilus LMG 18311 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsGuarnaccia, A.M. / Neiditch, M.B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of Streptococcus thermophilus SHP pheromone receptor Rgg3 in complex with Rgg3bp13
Authors: Guarnaccia, A.M. / Neiditch, M.B.
History
DepositionJan 26, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Positive transcriptional regulator MutR family
B: Rgg3bp13 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0649
Polymers35,3702
Non-polymers6957
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-73 kcal/mol
Surface area15630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.678, 111.678, 50.749
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Positive transcriptional regulator MutR family


Mass: 33242.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus thermophilus LMG 18311 (bacteria)
Gene: stu1044 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5M4D0
#2: Protein/peptide Rgg3bp13 peptide


Mass: 2127.510 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 129 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 100 mM sodium citrate pH 5.2, 300 mM Na/K tartrate, and 1.4 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU PhotonJet-S / Wavelength: 1.54056 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Nov 17, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 1.87→19.94 Å / Num. obs: 30196 / % possible obs: 99.4 % / Redundancy: 10.4 % / Biso Wilson estimate: 16.57 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.045 / Net I/σ(I): 16.08
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rpim(I) all% possible all
1.87-1.947.31.1129220.6530.29595.9
1.94-2.0210.22.430120.8370.19899.1
2.02-2.11114.3430380.9190.134100
2.11-2.2211.15.7130380.9590.106100
2.22-2.3611.17.2930380.9730.09100
2.36-2.55118.9130380.9810.079100
2.55-2.811113.1230380.990.056100
2.81-3.231121.130380.9960.034100
3.23-4.0910.741.6830380.9980.019100
4.09-19.949.555.8329960.9990.01398.6

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Processing

Software
NameVersionClassification
PHENIX2.0_5904refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→19.94 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 20.17
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2177 2802 10.13 %
Rwork0.183 24862 -
obs0.1865 27664 91.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.52 Å2
Refinement stepCycle: LAST / Resolution: 1.87→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2367 0 39 122 2528
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042444
X-RAY DIFFRACTIONf_angle_d0.6763296
X-RAY DIFFRACTIONf_chiral_restr0.037375
X-RAY DIFFRACTIONf_plane_restr0.006405
X-RAY DIFFRACTIONf_dihedral_angle_d15.432906
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.90.2857950.2836906X-RAY DIFFRACTION67
1.9-1.940.26411080.2526976X-RAY DIFFRACTION72
1.94-1.970.29131270.23431030X-RAY DIFFRACTION76
1.97-2.010.26331330.21141157X-RAY DIFFRACTION86
2.01-2.060.22921400.22061256X-RAY DIFFRACTION94
2.06-2.110.24081510.1961303X-RAY DIFFRACTION96
2.11-2.160.23981430.18881265X-RAY DIFFRACTION94
2.16-2.220.2261360.17881286X-RAY DIFFRACTION94
2.22-2.280.24161440.17441230X-RAY DIFFRACTION92
2.28-2.360.22871400.17871251X-RAY DIFFRACTION92
2.36-2.440.22541390.1831248X-RAY DIFFRACTION91
2.44-2.540.21991400.1811249X-RAY DIFFRACTION92
2.54-2.650.20931440.18451275X-RAY DIFFRACTION94
2.65-2.790.2131440.18371289X-RAY DIFFRACTION94
2.79-2.970.23811500.18511311X-RAY DIFFRACTION97
2.97-3.190.21181480.17881350X-RAY DIFFRACTION98
3.19-3.510.21241560.17221348X-RAY DIFFRACTION99
3.51-4.020.19151530.16121355X-RAY DIFFRACTION99
4.02-5.050.17451510.14571372X-RAY DIFFRACTION98
5.05-19.940.21151600.2011405X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.0248681629455-1.80810756265-0.930314190559223.329685380924-2.41635083572323.641941270327-0.034472059112741-1.2430334793196-0.164965253721790.1597937599438-0.25386741379455-1.4025467920167-0.366714327459891.51402803647690.236664082856630.36891050205629-0.079324840824434-0.0542979181886810.66217662942248-0.03933839647790.99322439315234-19.390306206943-14.120686061937-6.6902198939152
20.0113892502227580.0647757570461210.01440312029632.4159370036935-0.252474656330462.05848665008560.2437078002997-0.65233088628020.443031574842750.22778480523227-0.28213417509075-1.2065093849378-0.229669780744220.802781578325790.0129724831860070.32731230113966-0.078846957007770.137588338072780.42350452216117-0.0365310770177921.0122908395389-18.993773854836-6.5774748593239-12.850550515283
31.6324957465806-0.67520533885308-0.53249166032052.37452148087850.661227998914844.33571802132820.15361253409344-0.22601848673353-0.0500429525957470.48435727587135-0.10570332048291-0.0545959403248550.438521972290940.011412307084829-0.0430429596818140.27036812961471-0.092089869520169-0.043016874536870.16540216384301-0.0379315452254950.14341185203574-38.70744051076919.72709665563-6.9426252688065
41.86132126717310.66346922730006-0.506531350890731.1567120833136-0.176251071038580.98050168816615-0.0260147946203090.113205426495910.15983615777068-0.0134779111120750.0615845869189160.054718179000587-0.0879356900432710.0065716226971902-0.0103222801128680.174990405275770.0047016301840231-0.0171012459070610.0581345505982320.0203138144296420.082795114993084-51.78255819650214.133869407801-23.737728877387
56.4686022608168-0.520285802955521.10822728217198.3910317803686-4.95571360699267.62236021589160.028661918237983-0.277309509292550.700906764620420.200866761165170.249295791512830.49032031594179-0.68992951707154-0.70253431913698-0.285003927030090.3072725391999-2.508033393012E-7-0.0111702954928140.18442589198824-0.00679186233828030.27205591030586-52.57305986371215.752912528406-13.647111270511
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 6 through 23 )AA6 - 232 - 19
22chain 'A' and (resid 24 through 75 )AA24 - 7520 - 62
33chain 'A' and (resid 76 through 122 )AA76 - 12263 - 109
44chain 'A' and (resid 123 through 284 )AA123 - 284110 - 271
55chain 'B' and (resid 3 through 17 )BI3 - 171 - 15

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