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

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Basic information

Entry
Database: PDB / ID: 6exm
TitleThe Transcriptional Regulator PrfA from Listeria Monocytogenes in complex with a ring-fused 2-pyridone (MK202)
ComponentsListeriolysin positive regulatory factor A
KeywordsDNA BINDING PROTEIN / Transcription regulator / DNA binding / 2-pyridone / drug design / Listeria monocytogenes
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
ISOPROPYL ALCOHOL / Chem-QQH / Listeriolysin regulatory protein / Positive regulatory factor A
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGrundstrom, C. / Begum, A. / Hall, M. / 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
DepositionNov 8, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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 / _struct_conn.ptnr2_symmetry

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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)55,94311
Polymers54,9152
Non-polymers1,0289
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5600 Å2
ΔGint-50 kcal/mol
Surface area19790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.729, 88.647, 115.997
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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, UniProt: P22262*PLUS
#2: Chemical ChemComp-QQH / [(3~{R})-3-carboxy-7-[(2,3-dimethylphenyl)methyl]-5-oxidanylidene-2,3-dihydro-[1,3]thiazolo[3,2-a]pyridin-8-yl]-dimethyl-azanium


Mass: 359.463 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H23N2O3S
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.23 Å3/Da / Density % sol: 44.95 %
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: 0.992 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.992 Å / Relative weight: 1
ReflectionResolution: 1.6→48.534 Å / Num. obs: 65731 / % possible obs: 100 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 18.2
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 9 % / Rmerge(I) obs: 0.964 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F1R

5f1r


Resolution: 1.6→48.53 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.217 3187 4.85 %
Rwork0.182 --
obs0.184 65720 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→48.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3795 0 69 326 4190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123999
X-RAY DIFFRACTIONf_angle_d1.3285412
X-RAY DIFFRACTIONf_dihedral_angle_d15.3991462
X-RAY DIFFRACTIONf_chiral_restr0.059584
X-RAY DIFFRACTIONf_plane_restr0.006672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.62390.2971420.2732653X-RAY DIFFRACTION100
1.6239-1.64930.27481610.27622691X-RAY DIFFRACTION100
1.6493-1.67630.29941290.26042654X-RAY DIFFRACTION100
1.6763-1.70520.29591540.25662719X-RAY DIFFRACTION100
1.7052-1.73620.30211160.24662659X-RAY DIFFRACTION100
1.7362-1.76960.271240.23552730X-RAY DIFFRACTION100
1.7696-1.80570.22581420.22782657X-RAY DIFFRACTION100
1.8057-1.8450.2381400.2192682X-RAY DIFFRACTION100
1.845-1.88790.26561150.21192698X-RAY DIFFRACTION100
1.8879-1.93510.27131270.20982737X-RAY DIFFRACTION100
1.9351-1.98750.26311360.21582691X-RAY DIFFRACTION100
1.9875-2.04590.24711270.20452707X-RAY DIFFRACTION100
2.0459-2.1120.23951600.19662688X-RAY DIFFRACTION100
2.112-2.18750.21661280.19082717X-RAY DIFFRACTION100
2.1875-2.2750.25241580.18152701X-RAY DIFFRACTION100
2.275-2.37860.19651530.17832684X-RAY DIFFRACTION100
2.3786-2.5040.21131280.18032744X-RAY DIFFRACTION100
2.504-2.66090.23181460.18542726X-RAY DIFFRACTION100
2.6609-2.86630.20991400.18532706X-RAY DIFFRACTION100
2.8663-3.15470.21841410.18062771X-RAY DIFFRACTION100
3.1547-3.6110.21481440.17252760X-RAY DIFFRACTION100
3.611-4.5490.18031340.14592812X-RAY DIFFRACTION100
4.549-48.5560.18531420.16492946X-RAY DIFFRACTION100

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