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- PDB-6ev0: The Transcriptional Regulator PrfA from Listeria Monocytogenes in... -

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Basic information

Entry
Database: PDB / ID: 6ev0
TitleThe Transcriptional Regulator PrfA from Listeria Monocytogenes in complex with a ring-fused 2-pyridone (AC129)
ComponentsListeriolysin regulatory protein
KeywordsDNA BINDING PROTEIN / Transcription regulator / DNA binding / 2-pyridone / drug design / Listeria monocytogenes
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-like helix-turn-helix domain / Crp-type HTH domain profile. / Crp-type HTH domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A ...Transcription regulator HTH, Crp-type, conserved site / Crp-type HTH domain signature. / Crp-like helix-turn-helix domain / Crp-type HTH domain profile. / Crp-type HTH domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Jelly Rolls / Winged helix-like DNA-binding domain superfamily / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-BYK / Chem-C8N / ISOPROPYL ALCOHOL / Listeriolysin regulatory protein
Similarity search - Component
Biological speciesListeria monocytogenes EGD-e (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBegum, A. / Hall, M. / Grundstrom, C. / Cairns, A.G. / Kulen, M. / Lindgren, M. / Johansson, J. / Almqvist, F. / Sauer, U.H. / Sauer-Eriksson, A.E.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
Swedish Research Council Sweden
Citation
Journal: J. Med. Chem. / Year: 2018
Title: Structure-Based Design of Inhibitors Targeting PrfA, the Master Virulence Regulator of Listeria monocytogenes.
Authors: Kulen, M. / Lindgren, M. / Hansen, S. / Cairns, A.G. / Grundstrom, C. / Begum, A. / van der Lingen, I. / Brannstrom, K. / Hall, M. / Sauer, U.H. / Johansson, J. / Sauer-Eriksson, A.E. / Almqvist, F.
#1: Journal: Cell Chem Biol / Year: 2016
Title: Attenuating Listeria monocytogenes Virulence by Targeting the Regulatory Protein PrfA.
Authors: Good, J.A. / Andersson, C. / Hansen, S. / Wall, J. / Krishnan, K.S. / Begum, A. / Grundstrom, C. / Niemiec, M.S. / Vaitkevicius, K. / Chorell, E. / Wittung-Stafshede, P. / Sauer, U.H. / ...Authors: Good, J.A. / Andersson, C. / Hansen, S. / Wall, J. / Krishnan, K.S. / Begum, A. / Grundstrom, C. / Niemiec, M.S. / Vaitkevicius, K. / Chorell, E. / Wittung-Stafshede, P. / Sauer, U.H. / Sauer-Eriksson, A.E. / Almqvist, F. / Johansson, J.
History
DepositionOct 31, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 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

Downloads & links

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Assembly

Deposited unit
A: Listeriolysin regulatory protein
B: Listeriolysin regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1807
Polymers54,9152
Non-polymers1,2655
Water79344
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-26 kcal/mol
Surface area20550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.734, 80.514, 62.578
Angle α, β, γ (deg.)90.00, 113.93, 90.00
Int Tables number4
Space group name H-MP1211

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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 EGD-e (bacteria)
Strain: ATCC BAA-679 / EGD-e / Gene: prfA, lmo0200 / Production host: Escherichia coli (E. coli) / References: UniProt: P22262
#2: Chemical ChemComp-BYK / [(3~{R})-3-carboxy-7-(naphthalen-1-ylmethyl)-5-oxidanylidene-2,3-dihydro-[1,3]thiazolo[3,2-a]pyridin-8-yl]-dimethyl-azanium


Mass: 381.468 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H21N2O3S
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Chemical ChemComp-C8N / [(3~{S})-3-carboxy-7-(naphthalen-1-ylmethyl)-5-oxidanylidene-2,3-dihydro-[1,3]thiazolo[3,2-a]pyridin-8-yl]-dimethyl-azanium


Mass: 381.468 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H21N2O3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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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: 2.38 Å3/Da / Density % sol: 48.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PrfA was co-crystallized with complex (5 mol excess) using the hanging-drop vapor-diffusion technique. Crystals grew in 5 days after 2 microL of the protein solution (3.2-3.5 mg per ml PrfA, ...Details: PrfA was co-crystallized with complex (5 mol excess) using the hanging-drop vapor-diffusion technique. Crystals grew in 5 days after 2 microL of the protein solution (3.2-3.5 mg per ml PrfA, 200 mM NaCl, 20 mM NaP buffer, pH 6.5) was mixed with an equal volume of precipitant solution containing 20-24% PEG-4000, 17% isopropanol, 100 mM Na citrate pH 5.5 and allowed to equilibrate over a 1 ml solution of the precipitant in a Linbro plate (Hampton Research).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.3→43.6 Å / Num. obs: 22863 / % possible obs: 99.5 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 14.4
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.982 / Mean I/σ(I) obs: 2 / % possible all: 95.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F1R

5f1r


Resolution: 2.3→43.6 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.88
RfactorNum. reflection% reflection
Rfree0.263 1154 5.05 %
Rwork0.212 --
obs0.215 22855 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→43.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3801 0 89 44 3934
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024014
X-RAY DIFFRACTIONf_angle_d0.485436
X-RAY DIFFRACTIONf_dihedral_angle_d10.6062343
X-RAY DIFFRACTIONf_chiral_restr0.039584
X-RAY DIFFRACTIONf_plane_restr0.001670
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.40480.3941470.34182624X-RAY DIFFRACTION96
2.4048-2.53160.40651370.29822687X-RAY DIFFRACTION100
2.5316-2.69010.33971390.28312727X-RAY DIFFRACTION100
2.6901-2.89780.3111360.26052710X-RAY DIFFRACTION100
2.8978-3.18940.32471690.24882698X-RAY DIFFRACTION100
3.1894-3.65070.28781500.232730X-RAY DIFFRACTION100
3.6507-4.59870.21631540.18522719X-RAY DIFFRACTION100
4.5987-43.60480.19681220.16492806X-RAY DIFFRACTION100

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