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- PDB-5f1r: The Transcriptional Regulator PrfA from Listeria Monocytogenes in... -

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Basic information

Entry
Database: PDB / ID: 5f1r
TitleThe Transcriptional Regulator PrfA from Listeria Monocytogenes in complex with a ring-fused 2-pyridone (C10)
ComponentsListeriolysin regulatory protein
KeywordsDNA BINDING PROTEIN / PrfA / 2-pyridones / 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-like helix-turn-helix domain / 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-type HTH domain profile. / Crp-like helix-turn-helix domain / 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-42O / Listeriolysin regulatory protein
Similarity search - Component
Biological speciesListeria monocytogenes serovar 1/2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsBegum, A. / Grundstrom, C. / Good, J.A.D. / Andersson, C. / ALmqvist, F. / Johansson, J. / Sauer, U.H. / Sauer-Eriksson, A.E.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
Swedish Research Council Sweden
CitationJournal: 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
DepositionNov 30, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 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)55,4144
Polymers54,6592
Non-polymers7552
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-39 kcal/mol
Surface area20620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.340, 80.970, 62.340
Angle α, β, γ (deg.)90.00, 112.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Listeriolysin regulatory protein / Transcription regulatory protein PrfA


Mass: 27329.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (bacteria)
Gene: prfA, lmo0200 / Production host: Escherichia coli (E. coli) / References: UniProt: P22262
#2: Chemical ChemComp-42O / (3~{R})-8-cyclopropyl-7-(naphthalen-1-ylmethyl)-5-oxidanylidene-2,3-dihydro-[1,3]thiazolo[3,2-a]pyridine-3-carboxylic acid


Mass: 377.456 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H19NO3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PrfA was co-crystallized with complex 1 (5 mol excess). Crystals grew in 5 days after 1 microL of the protein solution (3.5 mg per ml PrfA, 200 mM NaCl, 20 mM NaP buffer, pH 6.5) was mixed ...Details: PrfA was co-crystallized with complex 1 (5 mol excess). Crystals grew in 5 days after 1 microL of the protein solution (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% PEG-4000, 16% isopropanol, 100 mM Na citrate pH 5.5 and allowed to equilibrate over a 1 ml solution of the precipitant in a Linbro plate. Before data collection, the crystals were transferred to a cryo-protectant solution including 16% glycerol in the precipitant solution.
PH range: 5.5-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.914 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.914 Å / Relative weight: 1
ReflectionResolution: 2.25→57.58 Å / Num. obs: 24400 / % possible obs: 99.2 % / Redundancy: 5.6 % / Biso Wilson estimate: 60.3 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 12.1
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.985 / Mean I/σ(I) obs: 1.6 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2beo

2beo


Resolution: 2.25→57.578 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2594 1991 8.16 %
Rwork0.1978 --
obs0.2029 24400 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80 Å2
Refinement stepCycle: LAST / Resolution: 2.25→57.578 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3738 0 54 22 3814
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143906
X-RAY DIFFRACTIONf_angle_d1.4635283
X-RAY DIFFRACTIONf_dihedral_angle_d10.5133637
X-RAY DIFFRACTIONf_chiral_restr0.073576
X-RAY DIFFRACTIONf_plane_restr0.012650
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2502-2.30650.44951310.38271561X-RAY DIFFRACTION97
2.3065-2.36880.35191520.34051584X-RAY DIFFRACTION99
2.3688-2.43850.36111340.3141604X-RAY DIFFRACTION99
2.4385-2.51730.36021440.26461585X-RAY DIFFRACTION99
2.5173-2.60720.31171440.23391595X-RAY DIFFRACTION99
2.6072-2.71160.32651480.23881593X-RAY DIFFRACTION100
2.7116-2.8350.29131280.21231617X-RAY DIFFRACTION99
2.835-2.98450.28691390.22141602X-RAY DIFFRACTION99
2.9845-3.17150.28231420.22891585X-RAY DIFFRACTION99
3.1715-3.41630.31361520.23151596X-RAY DIFFRACTION100
3.4163-3.760.28321470.20111604X-RAY DIFFRACTION100
3.76-4.3040.24051360.17411621X-RAY DIFFRACTION99
4.304-5.42190.20831440.16041620X-RAY DIFFRACTION100
5.4219-57.580.21361500.16821642X-RAY DIFFRACTION99

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