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- PDB-8cb5: The Transcriptional Regulator PrfA from Listeria Monocytogenes in... -

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Basic information

Entry
Database: PDB / ID: 8cb5
TitleThe Transcriptional Regulator PrfA from Listeria Monocytogenes in complex with tripeptide Glu-Val-Phe
Components
  • Listeriolysin regulatory protein
  • Tripeptide GLU-VAL-PHE
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
ISOPROPYL ALCOHOL / Listeriolysin regulatory protein
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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 GLU-VAL-PHE
D: Tripeptide GLU-VAL-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9289
Polymers55,7024
Non-polymers2265
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7100 Å2
ΔGint-62 kcal/mol
Surface area20100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.197, 87.306, 112.642
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


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 GLU-VAL-PHE


Mass: 393.434 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Listeria monocytogenes (bacteria)
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.13 Å3/Da / Density % sol: 42.18 %
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, 17% isopropanol, 16-26% ...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, 17% isopropanol, 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: MAX IV / Beamline: BioMAX / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.25→47.33 Å / Num. obs: 23242 / % possible obs: 100 % / Redundancy: 12.7 % / Biso Wilson estimate: 53.6 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.053 / Net I/σ(I): 12.9
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 13.4 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2263 / CC1/2: 0.546 / Rpim(I) all: 0.59 / % 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: 2.25→47.33 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2647 1161 5 %
Rwork0.2138 22081 -
obs0.2164 23242 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 140.64 Å2 / Biso mean: 69.4232 Å2 / Biso min: 33.58 Å2
Refinement stepCycle: final / Resolution: 2.25→47.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3716 0 14 53 3783
Biso mean--61.24 56.67 -
Num. residues----453
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.25-2.350.33891430.29727162859
2.35-2.480.35661420.27727092851
2.48-2.630.30431420.278827052847
2.63-2.830.29561440.248927422886
2.83-3.120.30811420.232727332875
3.12-3.570.29461460.212827472893
3.57-4.50.24451470.196828012948
4.5-47.330.22721550.191629283083

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