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- PDB-6ltz: Induced DNA bending by unique dimerization of HigA antitoxin -

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Basic information

Entry
Database: PDB / ID: 6ltz
TitleInduced DNA bending by unique dimerization of HigA antitoxin
ComponentsPutative antitoxin HigA3
KeywordsANTITOXIN
Function / homologyHelix-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 / DNA binding / DI(HYDROXYETHYL)ETHER / Putative antitoxin HigA3
Function and homology information
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.973 Å
AuthorsPark, J.Y. / Lee, B.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Iucrj / Year: 2020
Title: Induced DNA bending by unique dimerization of HigA antitoxin.
Authors: Park, J.Y. / Kim, H.J. / Pathak, C. / Yoon, H.J. / Kim, D.H. / Park, S.J. / Lee, B.J.
History
DepositionJan 23, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative antitoxin HigA3
B: Putative antitoxin HigA3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4187
Polymers25,7832
Non-polymers6355
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-19 kcal/mol
Surface area8740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.232, 84.232, 61.428
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Putative antitoxin HigA3


Mass: 12891.620 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: higA3, Rv3183 / Production host: Escherichia coli (E. coli) / References: UniProt: O53333
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.2 Å3/Da / Density % sol: 44.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1 M ammonium sulfate, 0.1 M HEPES, 0.5% w/v PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 15201 / % possible obs: 100 % / Redundancy: 3.5 % / Rrim(I) all: 0.06 / Net I/σ(I): 41.5
Reflection shellResolution: 1.97→2 Å / Num. unique obs: 762 / CC1/2: 0.978 / Rrim(I) all: 0.194

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Processing

Software
NameVersionClassification
PHENIX1.9refinement
PDB_EXTRACT3.25data extraction
DIFDATdata reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.973→32.113 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 23.06
RfactorNum. reflection% reflection
Rfree0.2337 727 4.79 %
Rwork0.1886 --
obs0.1906 15192 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.71 Å2 / Biso mean: 39.4561 Å2 / Biso min: 16.36 Å2
Refinement stepCycle: final / Resolution: 1.973→32.113 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1144 0 41 81 1266
Biso mean--51.9 43.53 -
Num. residues----154
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9732-2.12550.25241270.20262879X-RAY DIFFRACTION100
2.1255-2.33930.26631420.20032886X-RAY DIFFRACTION100
2.3393-2.67770.2371690.20482872X-RAY DIFFRACTION100
2.6777-3.3730.2371570.19992881X-RAY DIFFRACTION100
3.373-32.11670.21871320.17342947X-RAY DIFFRACTION100

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