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- PDB-5x6e: Crystal structure of PrfA-DNA binary complex -

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Basic information

Entry
Database: PDB / ID: 5x6e
TitleCrystal structure of PrfA-DNA binary complex
Components
  • DNA (28-MER)
  • DNA (29-MER)
  • Listeriolysin positive regulatory factor A
KeywordsDNA BINDING PROTEIN/DNA / DNA COMPLEX / DNA BINDING PROTEIN-DNA complex
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
GLUTATHIONE / DNA / DNA (> 10) / Listeriolysin regulatory protein / Positive regulatory factor A
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsWang, Y. / Feng, H. / Zhu, Y.L. / Gao, P.
CitationJournal: Protein Cell / Year: 2017
Title: Structural insights into glutathione-mediated activation of the master regulator PrfA in Listeria monocytogenes
Authors: Wang, Y. / Feng, H. / Zhu, Y. / Gao, P.
History
DepositionFeb 21, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
M: Listeriolysin positive regulatory factor A
N: Listeriolysin positive regulatory factor A
O: DNA (29-MER)
P: DNA (28-MER)
A: Listeriolysin positive regulatory factor A
B: Listeriolysin positive regulatory factor A
C: DNA (29-MER)
D: DNA (28-MER)
E: Listeriolysin positive regulatory factor A
F: Listeriolysin positive regulatory factor A
G: DNA (29-MER)
H: DNA (28-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,29718
Polymers217,45312
Non-polymers1,8446
Water00
1
M: Listeriolysin positive regulatory factor A
N: Listeriolysin positive regulatory factor A
O: DNA (29-MER)
P: DNA (28-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0996
Polymers72,4844
Non-polymers6152
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11310 Å2
ΔGint-104 kcal/mol
Surface area27510 Å2
MethodPISA
2
A: Listeriolysin positive regulatory factor A
B: Listeriolysin positive regulatory factor A
C: DNA (29-MER)
D: DNA (28-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0996
Polymers72,4844
Non-polymers6152
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11230 Å2
ΔGint-98 kcal/mol
Surface area28260 Å2
MethodPISA
3
E: Listeriolysin positive regulatory factor A
F: Listeriolysin positive regulatory factor A
G: DNA (29-MER)
H: DNA (28-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0996
Polymers72,4844
Non-polymers6152
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11200 Å2
ΔGint-104 kcal/mol
Surface area27940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.017, 96.590, 370.528
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: 27329.391 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: prfA, AJL40_05990, AJN46_04535, M643_11230 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4TVQ0, UniProt: P22262*PLUS
#2: DNA chain DNA (29-MER)


Mass: 8852.735 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Listeria monocytogenes (bacteria)
#3: DNA chain DNA (28-MER)


Mass: 8972.807 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Listeria monocytogenes (bacteria)
#4: Chemical
ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H17N3O6S

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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: 2.68 Å3/Da / Density % sol: 54.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Tris, 27% PEG3350, 0.2M Li2SO4, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.99→96.62 Å / Num. obs: 46496 / % possible obs: 88.8 % / Redundancy: 4.2 % / Net I/σ(I): 8.7

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.99→93.466 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 37.82
RfactorNum. reflection% reflection
Rfree0.2997 2352 5.06 %
Rwork0.2489 --
obs0.2515 46496 96.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.99→93.466 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11520 3514 120 0 15154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715836
X-RAY DIFFRACTIONf_angle_d1.27822134
X-RAY DIFFRACTIONf_dihedral_angle_d24.316126
X-RAY DIFFRACTIONf_chiral_restr0.0552436
X-RAY DIFFRACTIONf_plane_restr0.0052176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.99-3.05110.4385980.40052218X-RAY DIFFRACTION83
3.0511-3.11740.44171310.38652284X-RAY DIFFRACTION85
3.1174-3.18990.41161390.3612508X-RAY DIFFRACTION96
3.1899-3.26970.42011530.3492578X-RAY DIFFRACTION97
3.2697-3.35810.42061390.32562556X-RAY DIFFRACTION97
3.3581-3.45690.33231420.30842623X-RAY DIFFRACTION97
3.4569-3.56850.39091500.29562584X-RAY DIFFRACTION98
3.5685-3.69610.33831640.3012618X-RAY DIFFRACTION99
3.6961-3.84410.45821350.30722683X-RAY DIFFRACTION99
3.8441-4.0190.32841200.28172690X-RAY DIFFRACTION99
4.019-4.23090.33651200.26442654X-RAY DIFFRACTION99
4.2309-4.4960.28481490.24492606X-RAY DIFFRACTION96
4.496-4.84310.28481180.22962577X-RAY DIFFRACTION94
4.8431-5.33040.27971340.2312716X-RAY DIFFRACTION99
5.3304-6.10160.3021470.25592726X-RAY DIFFRACTION99
6.1016-7.68690.29951510.23952751X-RAY DIFFRACTION99
7.6869-93.51210.20861620.17672772X-RAY DIFFRACTION94

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