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- PDB-3g5o: The crystal structure of the toxin-antitoxin complex RelBE2 (Rv28... -

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Basic information

Entry
Database: PDB / ID: 3g5o
TitleThe crystal structure of the toxin-antitoxin complex RelBE2 (Rv2865-2866) from Mycobacterium tuberculosis
Components(Uncharacterized protein ...) x 2
KeywordsTOXIN/ANTITOXIN / heterotetramer / 1:1 ratio / Structural Genomics / PSI-2 / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC / Integrated Center for Structure and Function Innovation / ISFI / TOXIN-ANTITOXIN COMPLEX
Function / homology
Function and homology information


positive regulation of growth / toxin sequestering activity / negative regulation of growth / RNA catabolic process / endonuclease activity / Hydrolases; Acting on ester bonds / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Arc Repressor Mutant - #170 / YefM-like domain / Type II toxin-antitoxin system, antitoxin Phd/YefM / Antitoxin Phd_YefM, type II toxin-antitoxin system / YefM-like superfamily / YefM-like fold / ParE toxin of type II toxin-antitoxin system, parDE / RelE-like / Toxin-antitoxin system, RelE/ParE toxin family / YaeB-like fold ...Arc Repressor Mutant - #170 / YefM-like domain / Type II toxin-antitoxin system, antitoxin Phd/YefM / Antitoxin Phd_YefM, type II toxin-antitoxin system / YefM-like superfamily / YefM-like fold / ParE toxin of type II toxin-antitoxin system, parDE / RelE-like / Toxin-antitoxin system, RelE/ParE toxin family / YaeB-like fold / Toxin-antitoxin system, RelE/ParE toxin domain superfamily / Arc Repressor Mutant / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / THIOCYANATE ION / Antitoxin RelF / Toxin RelG
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsMiallau, L. / Cascio, D. / Eisenberg, D. / TB Structural Genomics Consortium (TBSGC) / Integrated Center for Structure and Function Innovation (ISFI)
CitationJournal: Structure / Year: 2013
Title: Comparative proteomics identifies the cell-associated lethality of M. tuberculosis RelBE-like toxin-antitoxin complexes.
Authors: Miallau, L. / Jain, P. / Arbing, M.A. / Cascio, D. / Phan, T. / Ahn, C.J. / Chan, S. / Chernishof, I. / Maxson, M. / Chiang, J. / Jacobs Jr., W.R. / Eisenberg, D.S.
History
DepositionFeb 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 23, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein Rv2865
B: Uncharacterized protein Rv2866
C: Uncharacterized protein Rv2866
D: Uncharacterized protein Rv2865
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2499
Polymers47,8724
Non-polymers3775
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9580 Å2
ΔGint-43.2 kcal/mol
Surface area17330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.540, 79.481, 86.278
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Uncharacterized protein ... , 2 types, 4 molecules ADBC

#1: Protein Uncharacterized protein Rv2865


Mass: 11859.122 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv2865 / Plasmid: pET46-Ek/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pRIL / References: UniProt: O33347
#2: Protein Uncharacterized protein Rv2866


Mass: 12076.865 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv2866 / Plasmid: pET46-Ek/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pRIL / References: UniProt: O33348

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Non-polymers , 6 types, 178 molecules

#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.53 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 25% PEG MME 2000, 0.15 M Potassium thiocyanate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1771
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-C10.9793
SYNCHROTRONALS 8.2.121
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 23, 2008
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SAD dataSINGLE WAVELENGTHMx-ray1
2Native dataSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
211
ReflectionResolution: 2→58.42 Å / Num. obs: 32091 / Observed criterion σ(I): 1.7 / Redundancy: 12.4 % / Biso Wilson estimate: 27.8 Å2 / Rsym value: 0.106 / Net I/σ(I): 24.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 13 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 4.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXDphasing
REFMAC5.5.0070refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2→58.42 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.915 / SU B: 3.363 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24553 1661 4.9 %RANDOM
Rwork0.20247 ---
obs0.20453 32091 94.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20 Å2
2---0.43 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 2→58.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2790 0 23 173 2986
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222898
X-RAY DIFFRACTIONr_angle_refined_deg1.4971.9783935
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7765360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.17221.765136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.80515495
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2821540
X-RAY DIFFRACTIONr_chiral_restr0.1080.2451
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212201
X-RAY DIFFRACTIONr_mcbond_it1.0931.51779
X-RAY DIFFRACTIONr_mcangle_it2.02922886
X-RAY DIFFRACTIONr_scbond_it2.96931119
X-RAY DIFFRACTIONr_scangle_it5.0474.51043
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 107 -
Rwork0.199 2259 -
obs-2259 90.48 %

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