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- PDB-8cb4: The Transcriptional Regulator PrfA from Listeria Monocytogenes in... -

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Basic information

Entry
Database: PDB / ID: 8cb4
TitleThe Transcriptional Regulator PrfA from Listeria Monocytogenes in complex with tripeptide Leu-Leu-Leu
Components
  • Listeriolysin regulatory protein
  • tripeptide LEU-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: 2.57 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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Listeriolysin regulatory protein
B: Listeriolysin regulatory protein
C: tripeptide LEU-LEU-LEU
D: tripeptide LEU-LEU-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6766
Polymers55,6304
Non-polymers462
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6270 Å2
ΔGint-79 kcal/mol
Surface area19860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.099, 86.785, 115.864
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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 tripeptide LEU-LEU-LEU


Mass: 357.489 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Listeria monocytogenes (bacteria)
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.17 Å3/Da / Density % sol: 43.41 %
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: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 2.57→48.1 Å / Num. obs: 15932 / % possible obs: 99.4 % / Redundancy: 4.6 % / Biso Wilson estimate: 53.1 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.099 / Net I/σ(I): 8
Reflection shellResolution: 2.57→2.66 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 1521 / CC1/2: 0.3 / Rpim(I) all: 0.927

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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: 2.57→44.42 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2765 793 4.98 %
Rwork0.2078 15118 -
obs0.2113 15911 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 167.65 Å2 / Biso mean: 73.4895 Å2 / Biso min: 21.72 Å2
Refinement stepCycle: final / Resolution: 2.57→44.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3790 0 2 36 3828
Biso mean--51.97 50 -
Num. residues----463
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.57-2.730.32621240.28392425254997
2.73-2.940.36451320.273524982630100
2.94-3.240.27461320.236425102642100
3.24-3.710.32661330.214225312664100
3.71-4.670.23541330.17382516264999
4.67-44.420.25471390.19262638277798

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