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

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Basic information

Entry
Database: PDB / ID: 6eut
TitleThe Transcriptional Regulator PrfA from Listeria Monocytogenes in complex with a ring-fused 2-pyridone (KSK67)
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-BY8 / ISOPROPYL ALCOHOL / Listeriolysin regulatory protein
Similarity search - Component
Biological speciesListeria monocytogenes EGD-e (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBegum, A. / Hall, M. / Grundstrom, C. / 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)55,8968
Polymers54,9152
Non-polymers9816
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-58 kcal/mol
Surface area19920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.934, 88.710, 116.788
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#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)
Gene: prfA, lmo0200 / Production host: Escherichia coli (E. coli) / References: UniProt: P22262

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Non-polymers , 5 types, 249 molecules

#2: Chemical ChemComp-BY8 / (3~{R})-8-cyclopropyl-7-[(4-methylnaphthalen-1-yl)methyl]-5-oxidanylidene-2,3-dihydro-[1,3]thiazolo[3,2-a]pyridine-3-carboxylic acid


Mass: 391.483 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H21NO3S
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.27 Å3/Da / Density % sol: 45.85 %
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: ID23-1 / Wavelength: 0.975 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.9→47.9 Å / Num. obs: 40105 / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 18.1
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.504 / Mean I/σ(I) obs: 3.3 / % possible all: 99.6

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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: 1.9→44.34 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.42
RfactorNum. reflection% reflection
Rfree0.228 1983 4.95 %
Rwork0.179 --
obs0.182 40038 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→44.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3795 0 68 243 4106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123984
X-RAY DIFFRACTIONf_angle_d1.135392
X-RAY DIFFRACTIONf_dihedral_angle_d13.7592344
X-RAY DIFFRACTIONf_chiral_restr0.064584
X-RAY DIFFRACTIONf_plane_restr0.007665
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94760.25461270.23582667X-RAY DIFFRACTION100
1.9476-2.00020.2911520.23172665X-RAY DIFFRACTION100
2.0002-2.05910.25411430.21662685X-RAY DIFFRACTION100
2.0591-2.12550.30661270.20792666X-RAY DIFFRACTION100
2.1255-2.20150.24461350.20472712X-RAY DIFFRACTION100
2.2015-2.28960.2251390.18882722X-RAY DIFFRACTION100
2.2896-2.39380.25611350.18132678X-RAY DIFFRACTION100
2.3938-2.520.23761410.18862705X-RAY DIFFRACTION100
2.52-2.67790.24581590.19282681X-RAY DIFFRACTION100
2.6779-2.88460.22461440.18552702X-RAY DIFFRACTION100
2.8846-3.17480.2391550.19192719X-RAY DIFFRACTION100
3.1748-3.63410.24051410.1772742X-RAY DIFFRACTION100
3.6341-4.57780.20871470.15142780X-RAY DIFFRACTION100
4.5778-44.35630.18571380.16182931X-RAY DIFFRACTION100

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