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- PDB-8cbg: The Transcriptional Regulator PrfA from Listeria Monocytogenes in... -

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Basic information

Entry
Database: PDB / ID: 8cbg
TitleThe Transcriptional Regulator PrfA from Listeria Monocytogenes in complex with tetrapeptide Arg-Gly-Leu-Leu
Components
  • Listeriolysin regulatory protein
  • peptide ARG-GLY-LEU-LEU
KeywordsTRANSCRIPTION / DNA BINDING PROTEIN / PRFA / LISTERIA INHIBITION / VIRULENCE
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding / cytosol
Similarity search - Function
Transcription regulator HTH, Crp-type, conserved site / Crp-type HTH domain signature. / Crp-type HTH domain profile. / Crp-type HTH domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Listeriolysin regulatory protein
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsOelker, M. / Sauer-Eriksson, A.E.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council2015-03607 Sweden
Swedish Research Council2019-03771 Sweden
Citation
Journal: Cell Rep / Year: 2025
Title: Structural basis of promiscuous inhibition of Listeria virulence activator PrfA by oligopeptides.
Authors: Hainzl, T. / Scortti, M. / Lindgren, C. / Grundstrom, C. / Krypotou, E. / Vazquez-Boland, J.A. / Sauer-Eriksson, A.E.
#1: Journal: Cell Rep / Year: 2019
Title: Control of Bacterial Virulence through the Peptide Signature of the Habitat.
Authors: Krypotou, E. / Scortti, M. / Grundstrom, C. / Oelker, M. / Luisi, B.F. / Sauer-Eriksson, A.E. / Vazquez-Boland, J.
History
DepositionJan 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Listeriolysin regulatory protein
B: Listeriolysin regulatory protein
C: peptide ARG-GLY-LEU-LEU
D: peptide ARG-GLY-LEU-LEU


Theoretical massNumber of molelcules
Total (without water)55,8324
Polymers55,8324
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-49 kcal/mol
Surface area21070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.518, 80.997, 60.458
Angle α, β, γ (deg.)90.00, 113.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Listeriolysin regulatory protein / Listeriolysin positive regulatory factor A / Pleitrophic regulatory factor A / Positive regulatory ...Listeriolysin positive regulatory factor A / Pleitrophic regulatory factor A / Positive regulatory factor A / PrfA / Transcriptional regulator


Mass: 27457.521 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: prfA, lmo0200 / Production host: Escherichia coli (E. coli) / References: UniProt: P22262
#2: Protein/peptide peptide ARG-GLY-LEU-LEU


Mass: 458.576 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Listeria monocytogenes (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.24 Å3/Da / Density % sol: 45.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Protein: 3.1-6.6 mg mL-1, 20 mM NaP pH 6.5, 200 mM NaCl was mixed with peptides (0.5-2.5% DMSO, 1-4 mM DTT) in ratio 1:10. Well solution: 100 mM Nacitrate pH 5.1-5.7, 16-26% PEG4000. ...Details: Protein: 3.1-6.6 mg mL-1, 20 mM NaP pH 6.5, 200 mM NaCl was mixed with peptides (0.5-2.5% DMSO, 1-4 mM DTT) in ratio 1:10. Well solution: 100 mM Nacitrate pH 5.1-5.7, 16-26% PEG4000. Dropsize 1:1 microL Cryoprotection: 35% PEG4000
PH range: 5.1-5.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→48.22 Å / Num. obs: 9945 / % possible obs: 100 % / Redundancy: 4.6 % / Biso Wilson estimate: 75.2 Å2 / CC1/2: 0.992 / Rpim(I) all: 0.086 / Net I/σ(I): 6.7
Reflection shellResolution: 3→3.18 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 978 / CC1/2: 0.431 / Rpim(I) all: 0.808 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→48.22 Å / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2825 807 8.11 %
Rwork0.2269 --
obs0.2314 9945 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→48.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3772 0 0 7 3779
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033852
X-RAY DIFFRACTIONf_angle_d0.5135198
X-RAY DIFFRACTIONf_dihedral_angle_d14.1571418
X-RAY DIFFRACTIONf_chiral_restr0.039575
X-RAY DIFFRACTIONf_plane_restr0.003645
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.190.38721330.36431517X-RAY DIFFRACTION99
3.19-3.430.39211340.28251510X-RAY DIFFRACTION100
3.43-3.780.31451340.24991515X-RAY DIFFRACTION100
3.78-4.330.28581340.20891520X-RAY DIFFRACTION100
4.33-5.450.26741340.2041527X-RAY DIFFRACTION100
5.45-48.220.22911380.1971549X-RAY DIFFRACTION100

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