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- PDB-6qvy: The Transcriptional Regulator PrfA-A94V mutant from Listeria Mono... -

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Basic information

Entry
Database: PDB / ID: 6qvy
TitleThe Transcriptional Regulator PrfA-A94V mutant from Listeria Monocytogenes
ComponentsListeriolysin regulatory protein
KeywordsDNA BINDING PROTEIN / TRANSCRIPTION REGULATOR / ACTIVATION / LISTERIA MONOCYTOGENES / TRANSCRIPTION / VIRULENCE FACTOR
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
ISOPROPYL ALCOHOL / : / Listeriolysin regulatory protein
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.686 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.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

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Assembly

Deposited unit
A: Listeriolysin regulatory protein
B: Listeriolysin regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,14411
Polymers54,7152
Non-polymers4309
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-41 kcal/mol
Surface area20510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.516, 88.571, 115.955
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 regulatory protein


Mass: 27357.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: prfa_2, DYZ77_02819 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3A7F3H1, UniProt: P22262*PLUS
#2: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#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.: 315 / 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: 44.84 %
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: 1.686→48.509 Å / Num. obs: 55743 / % possible obs: 99.5 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.04 / Net I/σ(I): 14.9
Reflection shellResolution: 1.69→1.75 Å / Redundancy: 12.8 % / Rmerge(I) obs: 1.76 / Num. unique obs: 5391 / Rpim(I) all: 0.72 / % possible all: 94

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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: 1.686→48.509 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.69
RfactorNum. reflection% reflection
Rfree0.2074 2769 4.97 %
Rwork0.1487 --
obs0.1516 55743 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.686→48.509 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3828 0 27 315 4170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014056
X-RAY DIFFRACTIONf_angle_d0.9925493
X-RAY DIFFRACTIONf_dihedral_angle_d12.3882404
X-RAY DIFFRACTIONf_chiral_restr0.058600
X-RAY DIFFRACTIONf_plane_restr0.005689
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6856-1.71470.36891010.24732493X-RAY DIFFRACTION94
1.7147-1.74580.33691410.21432614X-RAY DIFFRACTION100
1.7458-1.77940.27281500.19532617X-RAY DIFFRACTION100
1.7794-1.81570.28181340.17892609X-RAY DIFFRACTION100
1.8157-1.85520.24521240.17062636X-RAY DIFFRACTION100
1.8552-1.89840.23261640.16242628X-RAY DIFFRACTION100
1.8984-1.94590.28381360.16852593X-RAY DIFFRACTION100
1.9459-1.99850.26211340.16552674X-RAY DIFFRACTION100
1.9985-2.05730.20641570.14372616X-RAY DIFFRACTION100
2.0573-2.12370.23131500.14042616X-RAY DIFFRACTION100
2.1237-2.19960.24261230.14052651X-RAY DIFFRACTION100
2.1996-2.28760.21011370.13492656X-RAY DIFFRACTION100
2.2876-2.39180.19571430.13372632X-RAY DIFFRACTION98
2.3918-2.51790.22741320.13922588X-RAY DIFFRACTION97
2.5179-2.67560.18561290.14752655X-RAY DIFFRACTION100
2.6756-2.88220.2031290.14892688X-RAY DIFFRACTION100
2.8822-3.17210.20871500.14892704X-RAY DIFFRACTION100
3.1721-3.6310.23221360.14642698X-RAY DIFFRACTION100
3.631-4.57420.15051470.13012733X-RAY DIFFRACTION100
4.5742-48.5290.18481520.15562873X-RAY DIFFRACTION100

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