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- PDB-4pu8: Shewanella oneidensis Toxin Antitoxin System Antitoxin Protein Hi... -

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Basic information

Entry
Database: PDB / ID: 4pu8
TitleShewanella oneidensis Toxin Antitoxin System Antitoxin Protein HipB Resolution 2.35
ComponentsToxin-antitoxin system antidote transcriptional repressor Xre family
KeywordsTOXIN / Toxin Antitoxin System
Function / homology
Function and homology information


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
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsWen, Y. / Behiels, E. / Felix, J. / Elegheert, J. / Vergauwen, B. / Devreese, B. / Savvides, S.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: The bacterial antitoxin HipB establishes a ternary complex with operator DNA and phosphorylated toxin HipA to regulate bacterial persistence.
Authors: Wen, Y. / Behiels, E. / Felix, J. / Elegheert, J. / Vergauwen, B. / Devreese, B. / Savvides, S.N.
History
DepositionMar 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Toxin-antitoxin system antidote transcriptional repressor Xre family
A: Toxin-antitoxin system antidote transcriptional repressor Xre family


Theoretical massNumber of molelcules
Total (without water)25,9042
Polymers25,9042
Non-polymers00
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-16 kcal/mol
Surface area8060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.570, 71.570, 85.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Toxin-antitoxin system antidote transcriptional repressor Xre family


Mass: 12951.791 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-4 / Gene: Shewmr4_3396, SO_0705 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EIX4
#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: 1.59 Å3/Da / Density % sol: 22.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 0.1M Na HEPES pH7.5, 10% v/v 2-propanol, 20% PEG 4000, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→38.36 Å / Num. all: 45147 / Num. obs: 12674 / % possible obs: 99.71 % / Observed criterion σ(I): 2.15

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: dev_1287) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3DNV

3dnv


Resolution: 2.35→38.36 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 22.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2238 335 4.7 %
Rwork0.204 --
obs0.2049 7125 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→38.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1070 0 0 39 1109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041074
X-RAY DIFFRACTIONf_angle_d0.8781444
X-RAY DIFFRACTIONf_dihedral_angle_d13.042410
X-RAY DIFFRACTIONf_chiral_restr0.046188
X-RAY DIFFRACTIONf_plane_restr0.002176
Refinement TLS params.Method: refined / Origin x: 23.18 Å / Origin y: 21.3113 Å / Origin z: 34.0359 Å
111213212223313233
T0.3537 Å2-0.0389 Å2-0.0241 Å2-0.2848 Å2-0.0033 Å2--0.3534 Å2
L3.6065 °2-1.2788 °2-0.2918 °2-1.4822 °20.3022 °2--2.335 °2
S-0.0853 Å °0.2306 Å °-0.2206 Å °-0.0839 Å °0.0104 Å °0.0663 Å °0.1183 Å °0.0392 Å °0.0201 Å °
Refinement TLS groupSelection details: all

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