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- PDB-6t5i: The Transcriptional Regulator PrfA from Listeria Monocytogenes in... -

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Basic information

Entry
Database: PDB / ID: 6t5i
TitleThe Transcriptional Regulator PrfA from Listeria Monocytogenes in complex with inhibitor of WNT production (IWP)-2
ComponentsListeriolysin positive regulatory factor A
KeywordsTRANSCRIPTION / LISTERIA MONOCYTOGENES / DNA BINDING PROTEIN / INHIBITOR of WNT (IWP)
Function / homology
Function and homology information


positive regulation of single-species biofilm formation on inanimate substrate / DNA-binding transcription factor activity / DNA binding
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
Chem-9XK / Positive regulatory factor A
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsOelker, M. / Grundstrom, C. / Blumenthal, A. / Sauer-Eriksson, A.E.
Funding support Sweden, Australia, 2items
OrganizationGrant numberCountry
Swedish Research Council Sweden
National Health and Medical Research Council (Australia)GNT1142456 Australia
CitationJournal: Plos Pathog. / Year: 2022
Title: Inhibition of the master regulator of Listeria monocytogenes virulence enables bacterial clearance from spacious replication vacuoles in infected macrophages.
Authors: Tran, T.T. / Mathmann, C.D. / Gatica-Andrades, M. / Rollo, R.F. / Oelker, M. / Ljungberg, J.K. / Nguyen, T.T.K. / Zamoshnikova, A. / Kummari, L.K. / Wyer, O.J.K. / Irvine, K.M. / Melo- ...Authors: Tran, T.T. / Mathmann, C.D. / Gatica-Andrades, M. / Rollo, R.F. / Oelker, M. / Ljungberg, J.K. / Nguyen, T.T.K. / Zamoshnikova, A. / Kummari, L.K. / Wyer, O.J.K. / Irvine, K.M. / Melo-Bolivar, J. / Gross, A. / Brown, D. / Mak, J.Y.W. / Fairlie, D.P. / Hansford, K.A. / Cooper, M.A. / Giri, R. / Schreiber, V. / Joseph, S.R. / Simpson, F. / Barnett, T.C. / Johansson, J. / Dankers, W. / Harris, J. / Wells, T.J. / Kapetanovic, R. / Sweet, M.J. / Latomanski, E.A. / Newton, H.J. / Guerillot, R.J.R. / Hachani, A. / Stinear, T.P. / Ong, S.Y. / Chandran, Y. / Hartland, E.L. / Kobe, B. / Stow, J.L. / Sauer-Eriksson, A.E. / Begun, J. / Kling, J.C. / Blumenthal, A.
History
DepositionOct 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 19, 2022Group: Database references / Category: citation / citation_author
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
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Listeriolysin positive regulatory factor A
B: Listeriolysin positive regulatory factor A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,28716
Polymers54,9152
Non-polymers1,37214
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7310 Å2
ΔGint-31 kcal/mol
Surface area20110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.951, 92.667, 101.447
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 positive regulatory factor A / Listeriolysin positive regulatory protein / Listeriolysin regulatory protein / Pleitrophic ...Listeriolysin positive regulatory protein / Listeriolysin regulatory protein / 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, AJN46_04535, BWI22_01025 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4TVQ0
#2: Chemical ChemComp-9XK / ~{N}-(6-methyl-1,3-benzothiazol-2-yl)-2-[(4-oxidanylidene-3-phenyl-6,7-dihydrothieno[3,2-d]pyrimidin-2-yl)sulfanyl]ethanamide


Mass: 466.599 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H18N4O2S3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#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.: 101 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.05 Å3/Da / Density % sol: 40.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Purified PrfA, in 200 mM NaCl and 20 mM NaP buffer at pH 6.5 was mixed with 1 mM IWP2 and 3.7 mM DTT prior to crystallization. Droplets of 1 microL protein solution at 3.1 mg ml-1 were mixed ...Details: Purified PrfA, in 200 mM NaCl and 20 mM NaP buffer at pH 6.5 was mixed with 1 mM IWP2 and 3.7 mM DTT prior to crystallization. Droplets of 1 microL protein solution at 3.1 mg ml-1 were mixed with 1 microL reservoir solution consisting of 29 % (w/v) PEG 4000, 100 mM sodium citrate pH 5.5, and 18 % (v/v) isopropanol. The dimethyl sulfoxide (DMSO) concentration was kept at 10% (v/v). Prior to vitrification, crystals were equilibrated for 2 days in a solution containing 35 % (w/v) PEG 4000, 100 mM sodium citrate pH 5.5 and 1 mM IWP-2.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2→46.4 Å / Num. obs: 30998 / % possible obs: 99.2 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.04 / Net I/σ(I): 12.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 13.1 % / Rmerge(I) obs: 2.078 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3033 / CC1/2: 0.435 / Rpim(I) all: 0.609 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EUT

6eut


Resolution: 2→46.334 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.97
RfactorNum. reflection% reflection
Rfree0.2523 1550 5 %
Rwork0.1986 --
obs0.2012 30998 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 216.23 Å2 / Biso mean: 52.3169 Å2 / Biso min: 22.63 Å2
Refinement stepCycle: final / Resolution: 2→46.334 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3783 0 81 103 3967
Biso mean--62.4 47.37 -
Num. residues----464
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.06460.2971380.252261399
2.0646-2.13840.27381370.2401261299
2.1384-2.2240.28521380.2348262398
2.224-2.32520.26551380.2293262799
2.3252-2.44780.30291390.2387263799
2.4478-2.60110.29631390.2407265199
2.6011-2.80190.30391420.2271268899
2.8019-3.08390.26491400.2046266399
3.0839-3.530.27311420.1953270299
3.53-4.44680.21691460.16482751100
4.4468-46.3340.21921510.18552881100

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