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- PDB-4yg7: Structure of FL autorepression promoter complex -

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Basic information

Entry
Database: PDB / ID: 4yg7
TitleStructure of FL autorepression promoter complex
Components
  • (DNA (50-MER)) x 2
  • Antitoxin HipB
  • Serine/threonine-protein kinase HipA
KeywordsTRANSCRIPTION / TRANSFERASE/DNA / persistence / multidrug tolerance / autorepression / promoter / TRANSFERASE-DNA complex
Function / homology
Function and homology information


dormancy process / toxin-antitoxin complex / single-species biofilm formation / regulation of growth / DNA-binding transcription repressor activity / core promoter sequence-specific DNA binding / protein-DNA complex / sequence-specific DNA binding / non-specific serine/threonine protein kinase / transcription cis-regulatory region binding ...dormancy process / toxin-antitoxin complex / single-species biofilm formation / regulation of growth / DNA-binding transcription repressor activity / core promoter sequence-specific DNA binding / protein-DNA complex / sequence-specific DNA binding / non-specific serine/threonine protein kinase / transcription cis-regulatory region binding / response to antibiotic / protein serine kinase activity / negative regulation of DNA-templated transcription / protein serine/threonine kinase activity / DNA-templated transcription / regulation of DNA-templated transcription / magnesium ion binding / protein homodimerization activity / ATP binding / cytosol
Similarity search - Function
: / HipA, N-terminal subdomain 1 / HipA N-terminal domain / HipA-like, C-terminal / HipA-like C-terminal domain / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / lambda repressor-like DNA-binding domains / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain ...: / HipA, N-terminal subdomain 1 / HipA N-terminal domain / HipA-like, C-terminal / HipA-like C-terminal domain / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / lambda repressor-like DNA-binding domains / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Antitoxin HipB / Serine/threonine-protein kinase toxin HipA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.77 Å
AuthorsSchumacher, M.A.
CitationJournal: Nature / Year: 2015
Title: HipBA-promoter structures reveal the basis of heritable multidrug tolerance.
Authors: Schumacher, M.A. / Balani, P. / Min, J. / Chinnam, N.B. / Hansen, S. / Vulic, M. / Lewis, K. / Brennan, R.G.
History
DepositionFeb 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 1.2Apr 6, 2016Group: Source and taxonomy
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / exptl_crystal / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _exptl_crystal.density_Matthews / _exptl_crystal.density_percent_sol / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Antitoxin HipB
D: Serine/threonine-protein kinase HipA
E: Antitoxin HipB
R: DNA (50-MER)
T: DNA (50-MER)
C: Antitoxin HipB
G: Antitoxin HipB
K: Serine/threonine-protein kinase HipA


Theoretical massNumber of molelcules
Total (without water)160,9478
Polymers160,9478
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20960 Å2
ΔGint-118 kcal/mol
Surface area60700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)228.200, 228.200, 130.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
Antitoxin HipB


Mass: 8060.239 Da / Num. of mol.: 4 / Fragment: UNP residues 4-74
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: hipB, b1508, JW1501 / Production host: Escherichia coli (E. coli) / References: UniProt: P23873
#2: Protein Serine/threonine-protein kinase HipA / Ser/Thr-protein kinase HipA / Toxin HipA


Mass: 48946.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: hipA, b1507, JW1500 / Production host: Escherichia coli (E. coli)
References: UniProt: P23874, non-specific serine/threonine protein kinase
#3: DNA chain DNA (50-MER)


Mass: 15398.923 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#4: DNA chain DNA (50-MER)


Mass: 15414.922 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)

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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: 5.29 Å3/Da / Density % sol: 76.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: sodium formate / PH range: 5-7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 23, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.77→161.4 Å / Num. obs: 34997 / % possible obs: 63.6 % / Redundancy: 4 % / Net I/σ(I): 4
Reflection shellMean I/σ(I) obs: 1.4 / Rsym value: 0.762

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3DNV

3dnv


Resolution: 3.77→161.4 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: AUTHOR STATES ONLY MINIMAL REFINEMENT WAS PERFORMED.
RfactorNum. reflection% reflection
Rfree0.3785 2915 7.8 %
Rwork0.3837 32082 -
obs-34997 93.6 %
Solvent computationBsol: 72.4475 Å2
Displacement parametersBiso max: 267.11 Å2 / Biso mean: 180.4669 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1--64.878 Å20 Å20 Å2
2---64.878 Å20 Å2
3---129.757 Å2
Refinement stepCycle: final / Resolution: 3.77→161.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8763 2045 0 0 10808
Num. residues----1206
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_d1.406
X-RAY DIFFRACTIONc_mcbond_it3.8381.5
X-RAY DIFFRACTIONc_scbond_it3.7662
X-RAY DIFFRACTIONc_mcangle_it5.7252
X-RAY DIFFRACTIONc_scangle_it6.2652.5
LS refinement shellHighest resolution: 3.77 Å / Rfactor Rfree: 0.46
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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