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- PDB-3hzi: Structure of mdt protein -

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Basic information

Entry
Database: PDB / ID: 3hzi
TitleStructure of mdt protein
Components
  • 5'-D(*DAP*DCP*DTP*DAP*DTP*DCP*DCP*DCP*DCP*DTP*DTP*DAP*DAP*DGP*DGP*DGP*DGP*DAP*DTP*DAP*DG)-3'
  • HTH-type transcriptional regulator hipB
  • Protein hipA
KeywordsTranscription/DNA / mdt / persistence / DNA-binding / Repressor / Transcription / Transcription regulation / 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
ADENOSINE-5'-TRIPHOSPHATE / 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: 2.98 Å
AuthorsSchumacher, M.A.
CitationJournal: Science / Year: 2009
Title: Molecular mechanisms of HipA-mediated multidrug tolerance and its neutralization by HipB.
Authors: Schumacher, M.A. / Piro, K.M. / Xu, W. / Hansen, S. / Lewis, K. / Brennan, R.G.
History
DepositionJun 23, 2009Deposition site: RCSB / Processing site: RCSB
SupersessionJul 28, 2009ID: 3DNW
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 15, 2020Group: Derived calculations
Category: ndb_struct_na_base_pair / ndb_struct_na_base_pair_step ...ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / struct_conn
Item: _ndb_struct_na_base_pair.buckle / _ndb_struct_na_base_pair.hbond_type_12 ..._ndb_struct_na_base_pair.buckle / _ndb_struct_na_base_pair.hbond_type_12 / _ndb_struct_na_base_pair.hbond_type_28 / _ndb_struct_na_base_pair.j_symmetry / _ndb_struct_na_base_pair.opening / _ndb_struct_na_base_pair.propeller / _ndb_struct_na_base_pair.shear / _ndb_struct_na_base_pair.stagger / _ndb_struct_na_base_pair.stretch / _ndb_struct_na_base_pair_step.helical_rise / _ndb_struct_na_base_pair_step.helical_twist / _ndb_struct_na_base_pair_step.inclination / _ndb_struct_na_base_pair_step.j_symmetry_1 / _ndb_struct_na_base_pair_step.j_symmetry_2 / _ndb_struct_na_base_pair_step.rise / _ndb_struct_na_base_pair_step.roll / _ndb_struct_na_base_pair_step.shift / _ndb_struct_na_base_pair_step.slide / _ndb_struct_na_base_pair_step.tilt / _ndb_struct_na_base_pair_step.tip / _ndb_struct_na_base_pair_step.twist / _ndb_struct_na_base_pair_step.x_displacement / _ndb_struct_na_base_pair_step.y_displacement / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[3][3] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _pdbx_struct_oper_list.vector[1]
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein hipA
B: HTH-type transcriptional regulator hipB
T: 5'-D(*DAP*DCP*DTP*DAP*DTP*DCP*DCP*DCP*DCP*DTP*DTP*DAP*DAP*DGP*DGP*DGP*DGP*DAP*DTP*DAP*DG)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,36313
Polymers65,9913
Non-polymers1,37210
Water905
1
A: Protein hipA
B: HTH-type transcriptional regulator hipB
T: 5'-D(*DAP*DCP*DTP*DAP*DTP*DCP*DCP*DCP*DCP*DTP*DTP*DAP*DAP*DGP*DGP*DGP*DGP*DAP*DTP*DAP*DG)-3'
hetero molecules

A: Protein hipA
B: HTH-type transcriptional regulator hipB
T: 5'-D(*DAP*DCP*DTP*DAP*DTP*DCP*DCP*DCP*DCP*DTP*DTP*DAP*DAP*DGP*DGP*DGP*DGP*DAP*DTP*DAP*DG)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,72526
Polymers131,9826
Non-polymers2,74320
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)167.250, 167.250, 62.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number89
Space group name H-MP422

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Protein hipA


Mass: 49519.473 Da / Num. of mol.: 1 / Mutation: D309Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hipA, b1507, JW1500 / Plasmid: pBAD22 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P23874
#2: Protein HTH-type transcriptional regulator hipB


Mass: 10024.329 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hipB, b1508, JW1501 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P23873

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DNA chain , 1 types, 1 molecules T

#3: DNA chain 5'-D(*DAP*DCP*DTP*DAP*DTP*DCP*DCP*DCP*DCP*DTP*DTP*DAP*DAP*DGP*DGP*DGP*DGP*DAP*DTP*DAP*DG)-3'


Mass: 6447.187 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 3 types, 15 molecules

#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 3.31 Å3/Da / Density % sol: 62.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: tascimate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1tascimate11
2tascimate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.08 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 2, 2008 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.98→118.7 Å / Num. all: 18740 / Num. obs: 18730 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 156.3 Å2
Reflection shellResolution: 2.98→3.1 Å / Redundancy: 4 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.4 / % possible all: 99

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3DNV

3dnv


Resolution: 2.98→118.26 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1980011.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.283 2435 13.1 %RANDOM
Rwork0.265 ---
obs0.265 18552 99.3 %-
all-0 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.6207 Å2 / ksol: 0.355827 e/Å3
Displacement parametersBiso mean: 83 Å2
Baniso -1Baniso -2Baniso -3
1-19.12 Å20 Å20 Å2
2--19.12 Å20 Å2
3----38.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.77 Å0.69 Å
Refinement stepCycle: LAST / Resolution: 2.98→118.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3913 428 76 5 4422
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d1.09
LS refinement shellResolution: 2.98→3.17 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.409 395 13 %
Rwork0.373 2632 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5atp.paramatp-top.top

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