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- PDB-6lty: DNA bound antitoxin HigA3 -

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Basic information

Entry
Database: PDB / ID: 6lty
TitleDNA bound antitoxin HigA3
Components
  • DNA (5'-D(P*CP*CP*AP*CP*GP*AP*GP*AP*TP*AP*TP*AP*AP*CP*CP*TP*AP*GP*AP*G)-3')
  • DNA (5'-D(P*CP*TP*CP*TP*AP*GP*GP*TP*TP*AP*TP*AP*TP*CP*TP*CP*GP*TP*GP*G)-3')
  • Putative antitoxin HigA3
KeywordsANTITOXIN / DNA BINDING PROTEIN/DNA / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


HigA2-like, helix-turn-helix domain / Helix-turn-helix domain / 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
DNA / DNA (> 10) / Putative antitoxin HigA3
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.28 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
Revision 1.2Nov 29, 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: Putative antitoxin HigA3
B: Putative antitoxin HigA3
C: DNA (5'-D(P*CP*CP*AP*CP*GP*AP*GP*AP*TP*AP*TP*AP*AP*CP*CP*TP*AP*GP*AP*G)-3')
D: DNA (5'-D(P*CP*TP*CP*TP*AP*GP*GP*TP*TP*AP*TP*AP*TP*CP*TP*CP*GP*TP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)38,0504
Polymers38,0504
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7640 Å2
ΔGint-47 kcal/mol
Surface area14150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.615, 101.812, 58.027
Angle α, β, γ (deg.)90.000, 90.050, 90.000
Int Tables number5
Space group name H-MC121

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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: DNA chain DNA (5'-D(P*CP*CP*AP*CP*GP*AP*GP*AP*TP*AP*TP*AP*AP*CP*CP*TP*AP*GP*AP*G)-3')


Mass: 6136.008 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Mycobacterium tuberculosis H37Rv (bacteria)
#3: DNA chain DNA (5'-D(P*CP*TP*CP*TP*AP*GP*GP*TP*TP*AP*TP*AP*TP*CP*TP*CP*GP*TP*GP*G)-3')


Mass: 6130.961 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Mycobacterium tuberculosis H37Rv (bacteria)

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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: 2.9 Å3/Da / Density % sol: 57.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 23% w/v PEG3350, 0.2 M sodium acetate trihydrate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 3.277→50 Å / Num. obs: 6656 / % possible obs: 99.3 % / Redundancy: 2.6 % / Rrim(I) all: 0.072 / Net I/σ(I): 27.3
Reflection shellResolution: 3.277→3.36 Å / Num. unique obs: 316 / Rrim(I) all: 0.654

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LTZ

6ltz


Resolution: 3.28→41.79 Å / Cor.coef. Fo:Fc: 0.841 / Cor.coef. Fo:Fc free: 0.88 / SU B: 29.198 / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3256 337 5.1 %RANDOM
Rwork0.2774 ---
obs0.2799 6316 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 284.12 Å2 / Biso mean: 142.107 Å2 / Biso min: 77.14 Å2
Baniso -1Baniso -2Baniso -3
1-111.33 Å20 Å29.98 Å2
2---54.67 Å2-0 Å2
3----56.66 Å2
Refinement stepCycle: final / Resolution: 3.28→41.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1168 820 0 0 1988
Num. residues----196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122100
X-RAY DIFFRACTIONr_bond_other_d0.0020.0181591
X-RAY DIFFRACTIONr_angle_refined_deg1.4271.4123008
X-RAY DIFFRACTIONr_angle_other_deg1.3771.9873687
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6555154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.82620.96862
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.62615200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0181510
X-RAY DIFFRACTIONr_chiral_restr0.0670.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021822
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02442
LS refinement shellResolution: 3.28→3.362 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.383 31 -
Rwork0.24 416 -
obs--89.58 %

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