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- PDB-4yg1: HipB-O1-O2 complex/P21212 crystal form -

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Basic information

Entry
Database: PDB / ID: 4yg1
TitleHipB-O1-O2 complex/P21212 crystal form
Components
  • (DNA (48-MER)) x 2
  • Antitoxin HipB
KeywordsTRANSCRIPTION/DNA / persistence / multidrug tolerance / hipA / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


toxin-antitoxin complex / regulation of growth / DNA-binding transcription repressor activity / core promoter sequence-specific DNA binding / protein-DNA complex / sequence-specific DNA binding / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / DNA-templated transcription / regulation of DNA-templated transcription / protein homodimerization activity
Similarity search - Function
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
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.25 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 1.3Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
A: Antitoxin HipB
B: Antitoxin HipB
C: Antitoxin HipB
D: Antitoxin HipB
F: DNA (48-MER)
T: DNA (48-MER)


Theoretical massNumber of molelcules
Total (without water)62,3986
Polymers62,3986
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14950 Å2
ΔGint-103 kcal/mol
Surface area27560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)293.887, 54.460, 47.665
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Antitoxin HipB


Mass: 8209.449 Da / Num. of mol.: 4 / Fragment: UNP residues 1-72
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: DNA chain DNA (48-MER)


Mass: 14857.565 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: DNA chain DNA (48-MER)


Mass: 14702.517 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: 3.06 Å3/Da / Density % sol: 59.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 38% MPD, 0.1 M sodium acetate, pH 4.6 / PH range: 4.5-5.6

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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: Dec 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: 3.25→146.9 Å / Num. all: 13531 / Num. obs: 11197 / % possible obs: 95.6 % / Redundancy: 1.7 % / Net I/σ(I): 8
Reflection shellRmerge(I) obs: 0.327 / Mean I/σ(I) obs: 2

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Phasing

PhasingMethod: molecular replacement

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Processing

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

3dnv


Resolution: 3.25→146.9 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.287 1493 11 %
Rwork0.2461 9404 -
obs-10897 80.5 %
Solvent computationBsol: 47.1274 Å2
Displacement parametersBiso max: 172.04 Å2 / Biso mean: 110.3144 Å2 / Biso min: 60.86 Å2
Baniso -1Baniso -2Baniso -3
1--33.171 Å20 Å20 Å2
2--24.598 Å20 Å2
3---8.572 Å2
Refinement stepCycle: final / Resolution: 3.25→146.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2240 1962 0 0 4202
Num. residues----377
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d1.271
X-RAY DIFFRACTIONc_mcbond_it2.1361.5
X-RAY DIFFRACTIONc_scbond_it2.5162
X-RAY DIFFRACTIONc_mcangle_it3.692
X-RAY DIFFRACTIONc_scangle_it3.9952.5
LS refinement shellHighest resolution: 3.25 Å / Rfactor Rfree: 0.41
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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