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- PDB-5k98: Structure of HipA-HipB-O2-O3 complex -

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Basic information

Entry
Database: PDB / ID: 5k98
TitleStructure of HipA-HipB-O2-O3 complex
Components
  • Antitoxin HipB
  • DNA (5'-D(*CP*TP*AP*TP*CP*CP*CP*CP*TP*TP*AP*AP*GP*GP*GP*GP*AP*TP*AP*GP*GP*GP*A)-3')
  • DNA (5'-D(*TP*CP*CP*CP*TP*AP*TP*CP*CP*CP*CP*TP*TP*AP*AP*GP*GP*GP*GP*AP*TP*AP*G)-3')
  • Serine/threonine-protein kinase HipA
KeywordsTRANSCRIPTION/DNA / HipA / persistence / E. coli / TRANSCRIPTION-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 / phosphorylation / response to antibiotic / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of DNA-templated transcription / 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 / Cro/C1-type HTH domain profile. / lambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal 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 / Cro/C1-type HTH domain profile. / lambda repressor-like DNA-binding domains / 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 / Antitoxin HipB / Serine/threonine-protein kinase toxin HipA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Escherichia coli MP020980.2 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.99 Å
AuthorsSchumacher, M.
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
DepositionMay 31, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
A: Serine/threonine-protein kinase HipA
B: Antitoxin HipB
T: DNA (5'-D(*TP*CP*CP*CP*TP*AP*TP*CP*CP*CP*CP*TP*TP*AP*AP*GP*GP*GP*GP*AP*TP*AP*G)-3')
D: Serine/threonine-protein kinase HipA
P: Antitoxin HipB
E: DNA (5'-D(*CP*TP*AP*TP*CP*CP*CP*CP*TP*TP*AP*AP*GP*GP*GP*GP*AP*TP*AP*GP*GP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)135,6456
Polymers135,6456
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)214.036, 146.830, 53.751
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 Serine/threonine-protein kinase HipA / Ser/Thr-protein kinase HipA / Toxin HipA


Mass: 50423.859 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
#2: Protein Antitoxin HipB


Mass: 10337.615 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli MP020980.2 (bacteria) / Gene: hipB, ECMP0209802_2194 / Production host: Escherichia coli (E. coli) / References: UniProt: M9IJX7, UniProt: P23873*PLUS
#3: DNA chain DNA (5'-D(*TP*CP*CP*CP*TP*AP*TP*CP*CP*CP*CP*TP*TP*AP*AP*GP*GP*GP*GP*AP*TP*AP*G)-3')


Mass: 7016.537 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*CP*TP*AP*TP*CP*CP*CP*CP*TP*TP*AP*AP*GP*GP*GP*GP*AP*TP*AP*GP*GP*GP*A)-3')


Mass: 7105.599 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 3.1 Å3/Da / Density % sol: 60.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 1.3 M ammonium sulfate, 0.1 M citrate pH 5.6

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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: Aug 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.99→121.078 Å / Num. obs: 14049 / % possible obs: 92.2 % / Redundancy: 2 % / Net I/σ(I): 5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.6.4_486refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.99→121.078 Å / SU ML: 0.67 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 43.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.375 1401 10.01 %
Rwork0.35 --
obs0.352 13990 92.2 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 111.5 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 179.7 Å2
Baniso -1Baniso -2Baniso -3
1--42.0624 Å20 Å20 Å2
2---70.5635 Å20 Å2
3---112.6259 Å2
Refinement stepCycle: LAST / Resolution: 3.99→121.078 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7672 937 0 0 8609
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0158896
X-RAY DIFFRACTIONf_angle_d1.45712241
X-RAY DIFFRACTIONf_dihedral_angle_d20.3423378
X-RAY DIFFRACTIONf_chiral_restr0.0881386
X-RAY DIFFRACTIONf_plane_restr0.0061404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9901-4.13270.52031430.4771277X-RAY DIFFRACTION94
4.1327-4.29820.45581370.43481229X-RAY DIFFRACTION95
4.2982-4.49380.45291420.40261278X-RAY DIFFRACTION93
4.4938-4.73070.37751380.34361259X-RAY DIFFRACTION95
4.7307-5.02710.36381390.34531247X-RAY DIFFRACTION93
5.0271-5.41530.39251410.35211272X-RAY DIFFRACTION93
5.4153-5.96020.41941400.34981256X-RAY DIFFRACTION93
5.9602-6.82260.40371400.37171258X-RAY DIFFRACTION92
6.8226-8.59540.32871400.28271258X-RAY DIFFRACTION91
8.5954-121.13420.29551410.31161255X-RAY DIFFRACTION84

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