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- PDB-6qvz: The Transcriptional Regulator PrfA-L140H mutant from Listeria Mon... -

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Basic information

Entry
Database: PDB / ID: 6qvz
TitleThe Transcriptional Regulator PrfA-L140H mutant from Listeria Monocytogenes
ComponentsListeriolysin 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
ISOPROPYL ALCOHOL / Listeriolysin regulatory protein / PrfA
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.705 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 ...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)55,2749
Polymers54,9652
Non-polymers3097
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-50 kcal/mol
Surface area20550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.821, 88.465, 116.090
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 / Listeriolysin ...Listeriolysin positive regulatory protein / Listeriolysin regulatory protein / Listeriolysin transcriptional regulator PrfA / Pleitrophic regulatory factor A / Positive regulatory factor A / PrfA


Mass: 27482.510 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: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.24 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Droplets of 2 to 4 microl protein solution in 50 mM sodium phosphate pH 6.5 and 200 mM NaCl at 3 mg per ml were mixed with 2 microl reservoir solution consisting of 22-25% PEG 4000, 100 mM ...Details: Droplets of 2 to 4 microl protein solution in 50 mM sodium phosphate pH 6.5 and 200 mM NaCl at 3 mg per ml were mixed with 2 microl reservoir solution consisting of 22-25% PEG 4000, 100 mM sodium citrate pH 5.5, and 17% isopropanol.

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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: 2.7→48.5 Å / Num. obs: 13826 / % possible obs: 98.5 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.094 / Net I/σ(I): 8.4
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.715 / Mean I/σ(I) obs: 2 / Num. unique obs: 1733 / Rpim(I) all: 0.46 / % possible all: 94.7

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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: 5F1R

5f1r


Resolution: 2.705→44.216 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.63
RfactorNum. reflection% reflection
Rfree0.2539 706 5.13 %
Rwork0.1878 --
obs0.1913 13769 98.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.705→44.216 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3793 0 19 142 3954
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023923
X-RAY DIFFRACTIONf_angle_d0.4425300
X-RAY DIFFRACTIONf_dihedral_angle_d12.5112322
X-RAY DIFFRACTIONf_chiral_restr0.04580
X-RAY DIFFRACTIONf_plane_restr0.002660
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7055-2.91430.29741350.25012478X-RAY DIFFRACTION96
2.9143-3.20760.31571290.22162636X-RAY DIFFRACTION100
3.2076-3.67150.28991300.1972616X-RAY DIFFRACTION99
3.6715-4.62490.21791550.15982559X-RAY DIFFRACTION97
4.6249-44.22230.23761570.17712774X-RAY DIFFRACTION99

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