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- PDB-5jub: Crystal structure of ComR from S.thermophilus in complex with DNA... -

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Basic information

Entry
Database: PDB / ID: 5jub
TitleCrystal structure of ComR from S.thermophilus in complex with DNA and its signalling peptide ComS.
Components
  • ComS
  • Transcriptional regulator
  • pComX-for
  • pComX-rev
KeywordsTRANSCRIPTION / RNPP / Transcriptional activator / TPR domain / HTH domain / quorum-sensor / competence regulator
Function / homology
Function and homology information


ComR, tetratricopeptide / ComR tetratricopeptide / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / 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
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcriptional regulator
Similarity search - Component
Biological speciesStreptococcus thermophilus LMD-9 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsTalagas, A. / Fontaine, L. / Ledesma-Garcia, L. / Li de la Sierra-Gallay, I. / Hols, P. / Nessler, S.
CitationJournal: PLoS Pathog. / Year: 2016
Title: Structural Insights into Streptococcal Competence Regulation by the Cell-to-Cell Communication System ComRS.
Authors: Talagas, A. / Fontaine, L. / Ledesma-Garca, L. / Mignolet, J. / Li de la Sierra-Gallay, I. / Lazar, N. / Aumont-Nicaise, M. / Federle, M.J. / Prehna, G. / Hols, P. / Nessler, S.
History
DepositionMay 10, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator
B: Transcriptional regulator
C: ComS
D: ComS
X: pComX-rev
Z: pComX-for


Theoretical massNumber of molelcules
Total (without water)87,1266
Polymers87,1266
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10780 Å2
ΔGint-67 kcal/mol
Surface area32740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.110, 46.190, 100.270
Angle α, β, γ (deg.)90.00, 98.23, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Transcriptional regulator


Mass: 36547.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus thermophilus LMD-9 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold pLysS AG / References: UniProt: A0A1L1QK15*PLUS
#2: Protein/peptide ComS


Mass: 883.066 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Cognate signalling peptide of ComR
Source: (synth.) Streptococcus thermophilus LMD-9 (bacteria)
#3: DNA chain pComX-rev


Mass: 6141.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: ComR-box from ComX promoter
Source: (synth.) Streptococcus thermophilus LMD-9 (bacteria)
#4: DNA chain pComX-for


Mass: 6122.988 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: ComR-box from ComX promoter
Source: (synth.) Streptococcus thermophilus LMD-9 (bacteria)

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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: 2.45 Å3/Da / Density % sol: 49.75 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 30% PEG 550MME, 0.1M MgCl2, 0,05M Tris-HCl, pH=8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.978563 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978563 Å / Relative weight: 1
ReflectionResolution: 2.57→46.553 Å / Num. obs: 27134 / % possible obs: 99 % / Redundancy: 5.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.086 / Net I/σ(I): 13.31
Reflection shellResolution: 2.57→2.63 Å / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.81 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ComR apo

Resolution: 2.57→46.553 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2679 1355 5 %
Rwork0.2267 --
obs0.2288 27094 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.57→46.553 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5047 697 0 0 5744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025917
X-RAY DIFFRACTIONf_angle_d0.428115
X-RAY DIFFRACTIONf_dihedral_angle_d15.8783496
X-RAY DIFFRACTIONf_chiral_restr0.033914
X-RAY DIFFRACTIONf_plane_restr0.002905
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5699-2.66180.35621290.33562475X-RAY DIFFRACTION98
2.6618-2.76830.34151320.33132501X-RAY DIFFRACTION97
2.7683-2.89430.33641330.29262518X-RAY DIFFRACTION97
2.8943-3.04690.32651330.27332524X-RAY DIFFRACTION98
3.0469-3.23770.30881360.26722581X-RAY DIFFRACTION100
3.2377-3.48760.35441350.26472573X-RAY DIFFRACTION100
3.4876-3.83840.25641380.23072619X-RAY DIFFRACTION100
3.8384-4.39350.23521370.20472605X-RAY DIFFRACTION100
4.3935-5.53390.22751390.2072634X-RAY DIFFRACTION100
5.5339-46.5610.25071430.18962709X-RAY DIFFRACTION100

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