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- PDB-5lrr: The Transcriptional Regulator PrfA from Listeria Monocytogenes in... -

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Basic information

Entry
Database: PDB / ID: 5lrr
TitleThe Transcriptional Regulator PrfA from Listeria Monocytogenes in complex with glutathione
ComponentsListeriolysin positive regulatory factor A
KeywordsDNA BINDING PROTEIN / Transcription regulator / DNA binding / activation / glutathione / Listeria monocytogenes / transcription
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-type HTH domain profile. / Crp-like helix-turn-helix domain / 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-type HTH domain profile. / Crp-like helix-turn-helix domain / 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
GLUTATHIONE / HYDROGENPHOSPHATE ION / Listeriolysin regulatory protein / Positive regulatory factor A
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.171 Å
AuthorsHall, M. / Grundstrom, C. / Begum, A. / Lindberg, M. / Sauer, U.H. / Almqvist, F. / Johansson, J. / Sauer-Eriksson, A.E.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016
Title: Structural basis for glutathione-mediated activation of the virulence regulatory protein PrfA in Listeria.
Authors: Hall, M. / Grundstrom, C. / Begum, A. / Lindberg, M.J. / Sauer, U.H. / Almqvist, F. / Johansson, J. / Sauer-Eriksson, A.E.
History
DepositionAug 19, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Jan 11, 2017Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 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 positive regulatory factor A
B: Listeriolysin positive regulatory factor A
C: Listeriolysin positive regulatory factor A
D: Listeriolysin positive regulatory factor A
E: Listeriolysin positive regulatory factor A
F: Listeriolysin positive regulatory factor A
G: Listeriolysin positive regulatory factor A
H: Listeriolysin positive regulatory factor A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,49724
Polymers218,6358
Non-polymers2,86116
Water9,080504
1
A: Listeriolysin positive regulatory factor A
B: Listeriolysin positive regulatory factor A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5848
Polymers54,6592
Non-polymers9266
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6500 Å2
ΔGint-80 kcal/mol
Surface area19690 Å2
MethodPISA
2
C: Listeriolysin positive regulatory factor A
D: Listeriolysin positive regulatory factor A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2965
Polymers54,6592
Non-polymers6383
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-65 kcal/mol
Surface area20090 Å2
MethodPISA
3
E: Listeriolysin positive regulatory factor A
F: Listeriolysin positive regulatory factor A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3196
Polymers54,6592
Non-polymers6614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6070 Å2
ΔGint-77 kcal/mol
Surface area20390 Å2
MethodPISA
4
G: Listeriolysin positive regulatory factor A
H: Listeriolysin positive regulatory factor A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2965
Polymers54,6592
Non-polymers6383
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-63 kcal/mol
Surface area20070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.265, 184.227, 100.457
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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


Mass: 27329.391 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: prfA, M643_11230 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4TVQ0, UniProt: P22262*PLUS
#2: Chemical
ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PI / HYDROGENPHOSPHATE ION


Mass: 95.979 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: HO4P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 504 / 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: 2.46 Å3/Da / Density % sol: 50.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Prior to the crystallization setup GSH and DTT were added to the protein solution to final concentrations of 5 mM and 1 mM, respectively. Droplets of 4 microL protein solution at 3.2 mg per ...Details: Prior to the crystallization setup GSH and DTT were added to the protein solution to final concentrations of 5 mM and 1 mM, respectively. Droplets of 4 microL protein solution at 3.2 mg per ml were mixed with 2 microL reservoir solution consisting of 22% PEG 4000, 100 mM sodium citrate pH 5.5. Crystals used for data collection were obtained after 48 h. Prior to vitrification crystals were equilibrated for 24 h in a solution containing 30% PEG 4000, 100 mM sodium citrate pH 5.5 and 50 mM GSH.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.073 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.073 Å / Relative weight: 1
ReflectionResolution: 2.17→48.538 Å / Num. obs: 114028 / % possible obs: 99.6 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 13.2
Reflection shellResolution: 2.17→2.25 Å / Redundancy: 13.1 % / Rmerge(I) obs: 1.84 / Mean I/σ(I) obs: 1.5 / % possible all: 96.7

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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: 2bgc

2bgc


Resolution: 2.171→48.538 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.47
RfactorNum. reflection% reflection
Rfree0.2406 5706 5.01 %
Rwork0.2075 --
obs0.2092 113945 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.171→48.538 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15247 0 180 504 15931
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00315792
X-RAY DIFFRACTIONf_angle_d0.50821329
X-RAY DIFFRACTIONf_dihedral_angle_d12.0929286
X-RAY DIFFRACTIONf_chiral_restr0.0412339
X-RAY DIFFRACTIONf_plane_restr0.0022658
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1705-2.19520.37971700.33523275X-RAY DIFFRACTION91
2.1952-2.2210.32741840.30353567X-RAY DIFFRACTION100
2.221-2.24810.34421920.29323555X-RAY DIFFRACTION100
2.2481-2.27660.31732080.2933554X-RAY DIFFRACTION100
2.2766-2.30650.3461820.27863603X-RAY DIFFRACTION100
2.3065-2.33810.32462000.26673535X-RAY DIFFRACTION100
2.3381-2.37150.30261730.26933623X-RAY DIFFRACTION100
2.3715-2.40690.29792000.26673557X-RAY DIFFRACTION100
2.4069-2.44450.30561880.25653602X-RAY DIFFRACTION100
2.4445-2.48460.2881790.25253587X-RAY DIFFRACTION100
2.4846-2.52750.31921980.25783609X-RAY DIFFRACTION100
2.5275-2.57340.29511970.24583558X-RAY DIFFRACTION100
2.5734-2.62290.29551710.23573584X-RAY DIFFRACTION100
2.6229-2.67640.30251810.24613613X-RAY DIFFRACTION100
2.6764-2.73460.28511750.23693621X-RAY DIFFRACTION100
2.7346-2.79820.25771740.23013646X-RAY DIFFRACTION100
2.7982-2.86820.28341760.22953595X-RAY DIFFRACTION100
2.8682-2.94570.28242030.24233585X-RAY DIFFRACTION100
2.9457-3.03240.30951980.24083595X-RAY DIFFRACTION100
3.0324-3.13030.24492010.24353632X-RAY DIFFRACTION100
3.1303-3.24210.25431880.22483616X-RAY DIFFRACTION100
3.2421-3.37190.26451980.22053601X-RAY DIFFRACTION100
3.3719-3.52530.23541950.21083624X-RAY DIFFRACTION100
3.5253-3.71110.2421810.20193638X-RAY DIFFRACTION100
3.7111-3.94350.24162090.19893639X-RAY DIFFRACTION100
3.9435-4.24790.20332060.16763621X-RAY DIFFRACTION100
4.2479-4.6750.17641740.15043685X-RAY DIFFRACTION100
4.675-5.35080.18622000.15453699X-RAY DIFFRACTION100
5.3508-6.73860.19671920.18753742X-RAY DIFFRACTION100
6.7386-48.54960.19712130.18293878X-RAY DIFFRACTION100

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