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- PDB-6hpc: Crystal structure of the HicB antitoxin from E. coli -

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Basic information

Entry
Database: PDB / ID: 6hpc
TitleCrystal structure of the HicB antitoxin from E. coli
ComponentsAntitoxin HicB
KeywordsANTITOXIN / dna binding / helix-turn-helix / HTH
Function / homology
Function and homology information


toxin-antitoxin complex / regulation of growth / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
HicB-like antitoxin of toxin-antitoxin system / HicB_like antitoxin of bacterial toxin-antitoxin system / TTHA1013/TTHA0281-like / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily
Similarity search - Domain/homology
Antitoxin HicB / Antitoxin HicB
Similarity search - Component
Biological speciesEscherichia coli 2-210-07_S3_C3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.26 Å
AuthorsManav, M.C. / Brodersen, D.E.
Funding support Denmark, 2items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF17OC0030646 Denmark
Danish National Research FoundationDNRF120 Denmark
CitationJournal: Structure / Year: 2019
Title: The E. coli HicB Antitoxin Contains a Structurally Stable Helix-Turn-Helix DNA Binding Domain.
Authors: Manav, M.C. / Turnbull, K.J. / Jurenas, D. / Garcia-Pino, A. / Gerdes, K. / Brodersen, D.E.
History
DepositionSep 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_CC_half
Revision 1.2Nov 13, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Antitoxin HicB
A: Antitoxin HicB


Theoretical massNumber of molelcules
Total (without water)30,8982
Polymers30,8982
Non-polymers00
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-21 kcal/mol
Surface area15010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.090, 60.380, 59.340
Angle α, β, γ (deg.)90.000, 103.760, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Antitoxin HicB


Mass: 15449.135 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli 2-210-07_S3_C3 (bacteria)
Gene: hicB, AC45_3823 / Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A070SL92, UniProt: P67697*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.46 Å3/Da / Density % sol: 49.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 4 % Tacsimate 12 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.26→57.64 Å / Num. obs: 13836 / % possible obs: 98.83 % / Redundancy: 3.4 % / Biso Wilson estimate: 85.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.033 / Net I/σ(I): 1.18
Reflection shellResolution: 2.26→2.341 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.1082 / Mean I/σ(I) obs: 1.18 / Num. unique obs: 1363 / CC1/2: 0.526 / % possible all: 98.62

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Processing

Software
NameClassification
XDSdata reduction
XSCALEdata scaling
CRANK2phasing
PHENIXrefinement
RefinementMethod to determine structure: SAD / Resolution: 2.26→57.64 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.2679 --random
Rwork0.2266 ---
obs-13822 98.83 %-
Displacement parametersBiso mean: 85.4 Å2
Refinement stepCycle: LAST / Resolution: 2.26→57.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2146 0 0 39 2185

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