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- PDB-6qwm: The Transcriptional Regulator PrfA-A218G mutant from Listeria Mon... -

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Basic information

Entry
Database: PDB / ID: 6qwm
TitleThe Transcriptional Regulator PrfA-A218G mutant from Listeria Monocytogenes in complex with a 30-bp operator PrfA-box motif
Components
  • (DNA (30-MER)) x 2
  • Listeriolysin positive regulatory factor A
KeywordsDNA BINDING PROTEIN / TRANSCRIPTION REGULATOR / ACTIVATION / LISTERIA MONOCYTOGENES / TRANSCRIPTION / VIRULENCE FACTOR
Function / homology
Function and homology information


positive regulation of single-species biofilm formation on inanimate substrate / 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
DNA / DNA (> 10) / Listeriolysin regulatory protein / Positive regulatory factor A
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsHall, M. / Grundstrom, C. / Hansen, S. / Brannstrom, K. / Johansson, J. / Sauer-Eriksson, A.E.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: J.Bacteriol. / Year: 2020
Title: A Novel Growth-Based Selection Strategy Identifies New Constitutively Active Variants of the Major Virulence Regulator PrfA in Listeria monocytogenes.
Authors: Hansen, S. / Hall, M. / Grundstrom, C. / Brannstrom, K. / Sauer-Eriksson, A.E. / Johansson, J.
History
DepositionMar 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Jan 24, 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 positive regulatory factor A
B: Listeriolysin positive regulatory factor A
C: DNA (30-MER)
D: DNA (30-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6057
Polymers73,3294
Non-polymers2763
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10830 Å2
ΔGint-86 kcal/mol
Surface area28510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.628, 78.628, 265.122
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Listeriolysin positive regulatory factor A / Listeriolysin positive regulatory protein / Listeriolysin regulatory protein / Listeriolysin ...Listeriolysin positive regulatory protein / Listeriolysin regulatory protein / Listeriolysin transcriptional regulator PrfA / Pleitrophic regulatory factor A / Positive regulatory factor A / PrfA


Mass: 27443.494 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: prfA, CDR86_15285, D3B95_15085, DOE67_09655 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4TVQ0, UniProt: P22262*PLUS
#2: DNA chain DNA (30-MER)


Mass: 9261.000 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Listeria monocytogenes (bacteria)
#3: DNA chain DNA (30-MER)


Mass: 9180.953 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Listeria monocytogenes (bacteria)
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.79 Å3/Da / Density % sol: 55.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Droplets of 4 microl protein-DNA solution (ratio 1:1.3) in 20 mM Tris-HCl pH 8.0, 50 mM NaCl, and 1 mM EDTA at 6 mg per ml were mixed with 2 microl reservoir solution consisting of 8% PEG ...Details: Droplets of 4 microl protein-DNA solution (ratio 1:1.3) in 20 mM Tris-HCl pH 8.0, 50 mM NaCl, and 1 mM EDTA at 6 mg per ml were mixed with 2 microl reservoir solution consisting of 8% PEG 8000, 100 mM sodium citrate pH 4.6, 100 mM Magnesium acetate and 20% glycerol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.9→47.1 Å / Num. obs: 19313 / % possible obs: 99.8 % / Redundancy: 25.7 % / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.038 / Net I/σ(I): 18.2
Reflection shellResolution: 2.9→3 Å / Redundancy: 27.8 % / Rmerge(I) obs: 0.976 / Mean I/σ(I) obs: 4 / Num. unique obs: 1891 / Rpim(I) all: 0.261 / % possible all: 99.9

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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: 5LEJ

5lej


Resolution: 2.9→47.06 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.29 917 4.79 %
Rwork0.2339 --
obs0.2365 19125 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→47.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3838 1230 18 11 5097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035331
X-RAY DIFFRACTIONf_angle_d0.5337458
X-RAY DIFFRACTIONf_dihedral_angle_d17.792931
X-RAY DIFFRACTIONf_chiral_restr0.039823
X-RAY DIFFRACTIONf_plane_restr0.002723
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.05290.41391320.33332538X-RAY DIFFRACTION100
3.0529-3.24410.33931090.27352517X-RAY DIFFRACTION97
3.2441-3.49450.33981370.27042508X-RAY DIFFRACTION98
3.4945-3.8460.33221310.25012552X-RAY DIFFRACTION99
3.846-4.40220.30251320.22152619X-RAY DIFFRACTION100
4.4022-5.54490.2551330.21212659X-RAY DIFFRACTION100
5.5449-47.0660.24161430.21192815X-RAY DIFFRACTION99

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