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- PDB-7yk3: Crystal structure of DarTG toxin-antitoxin complex from Mycobacte... -

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Basic information

Entry
Database: PDB / ID: 7yk3
TitleCrystal structure of DarTG toxin-antitoxin complex from Mycobacterium tuberculosis
Components
  • DNA ADP-ribosyl glycohydrolase
  • DNA ADP-ribosyl transferase
KeywordsTOXIN / DarT-DarG complex / Toxin-Antitoxin complex / Mycobacterium tuberculosis
Function / homology
Function and homology information


ADP-ribosyl-[dinitrogen reductase] hydrolase activity / purine nucleoside metabolic process / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / glycosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / nucleotidyltransferase activity / DNA damage response / DNA binding / cytosol
Similarity search - Function
ssDNA thymidine ADP-ribosyltransferase, DarT / ssDNA thymidine ADP-ribosyltransferase, DarT / DNA ADP-ribosyl transferase (DarT) domain profile. / : / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like
Similarity search - Domain/homology
PHOSPHATE ION / DNA ADP-ribosyl transferase / DNA ADP-ribosyl glycohydrolase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDeep, A. / Kaur, J. / Singh, L. / Thakur, K.G.
Funding support India, 2items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research (CSIR) India
Department of Science & Technology (DST, India)EMR/2016/003728 India
CitationJournal: Structure / Year: 2023
Title: Structural insights into DarT toxin neutralization by cognate DarG antitoxin: ssDNA mimicry by DarG C-terminal domain keeps the DarT toxin inhibited.
Authors: Deep, A. / Singh, L. / Kaur, J. / Velusamy, M. / Bhardwaj, P. / Singh, R. / Thakur, K.G.
History
DepositionJul 21, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / refine
Item: _refine.pdbx_starting_model
Revision 1.3Nov 15, 2023Group: Structure summary / Category: audit_author
Revision 1.4Dec 18, 2024Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA ADP-ribosyl transferase
B: DNA ADP-ribosyl glycohydrolase
C: DNA ADP-ribosyl transferase
D: DNA ADP-ribosyl glycohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,5526
Polymers95,3624
Non-polymers1902
Water5,927329
1
A: DNA ADP-ribosyl transferase
B: DNA ADP-ribosyl glycohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7763
Polymers47,6812
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-12 kcal/mol
Surface area17490 Å2
MethodPISA
2
C: DNA ADP-ribosyl transferase
D: DNA ADP-ribosyl glycohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7763
Polymers47,6812
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-11 kcal/mol
Surface area17410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.530, 54.550, 93.090
Angle α, β, γ (deg.)105.03, 93.10, 102.69
Int Tables number1
Space group name H-MP1

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Components

#1: Protein DNA ADP-ribosyl transferase / DarT / Toxin DarT / DarT domain-containing protein


Mass: 26844.420 Da / Num. of mol.: 2 / Mutation: E183A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: darT, Rv0059 / Plasmid: pET DuetN-Rv0059 / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta(DE3)
References: UniProt: O53604, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Protein DNA ADP-ribosyl glycohydrolase / DarG / Antitoxin DarG / Macro domain-containing protein


Mass: 20836.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: darG, Rv0060 / Plasmid: pETDuetN-Rv0060 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta
References: UniProt: O53605, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 1.47 Å3/Da / Density % sol: 16.49 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / pH: 7.5 / Details: 0.1 M NaHEPES, 20% w/v PEG 10000 / PH range: 6.5 - 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 21, 2019 / Details: LN2 closed loop cooling
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.2→34.48 Å / Num. obs: 34943 / % possible obs: 92.2 % / Redundancy: 3 % / CC1/2: 0.979 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.077 / Rrim(I) all: 0.135 / Χ2: 0.55 / Net I/σ(I): 5.5 / Num. measured all: 103813
Reflection shellResolution: 2.2→2.27 Å / % possible obs: 91.4 % / Redundancy: 3 % / Rmerge(I) obs: 0.649 / Num. measured all: 9078 / Num. unique obs: 3045 / CC1/2: 0.606 / Rpim(I) all: 0.455 / Rrim(I) all: 0.798 / Χ2: 0.52 / Net I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
AimlessCCP4i 7.0.053data scaling
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7OMY for DarT and RoseTTAFold predicted model for DarG

7omy


Resolution: 2.2→34.48 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 27.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2499 1726 4.95 %
Rwork0.1788 --
obs0.1823 34901 92.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→34.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6361 0 10 329 6700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086522
X-RAY DIFFRACTIONf_angle_d0.98874
X-RAY DIFFRACTIONf_dihedral_angle_d21.779916
X-RAY DIFFRACTIONf_chiral_restr0.052977
X-RAY DIFFRACTIONf_plane_restr0.0091150
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.37011470.32672739X-RAY DIFFRACTION90
2.26-2.340.29021230.24542673X-RAY DIFFRACTION89
2.34-2.420.2941210.20542598X-RAY DIFFRACTION86
2.42-2.520.3061440.20322804X-RAY DIFFRACTION93
2.52-2.630.30311550.20452774X-RAY DIFFRACTION93
2.63-2.770.28321470.20242817X-RAY DIFFRACTION94
2.77-2.950.23751670.18982819X-RAY DIFFRACTION95
2.95-3.170.25891340.18062614X-RAY DIFFRACTION87
3.17-3.490.25131490.1672808X-RAY DIFFRACTION95
3.49-40.22841460.15262927X-RAY DIFFRACTION96
4-5.030.20711500.14482828X-RAY DIFFRACTION94
5.03-34.480.20771430.15492774X-RAY DIFFRACTION93
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.95561.01910.400710.02335.47368.4966-0.12330.48260.0514-0.9384-0.070.3096-0.3713-0.30060.16280.2074-0.0258-0.04530.18490.0840.189323.244546.135210.8242
25.57874.3202-3.1182.5696-2.88524.89830.1443-0.52570.71820.6731-0.05560.0157-0.55820.0408-0.05210.2810.0042-0.09950.2935-0.06070.351527.269243.372728.6061
32.10540.04070.15465.4801-2.1312.769-0.08970.04830.1206-0.03880.12090.3889-0.0662-0.1361-0.03840.1765-0.0434-0.03630.1462-0.05610.232422.3342.163219.4149
46.42032.2954-0.36376.63350.88653.5721-0.29250.76780.1784-0.51270.07440.42790.116-0.36030.18630.2286-0.0078-0.04410.1858-0.00430.190817.280332.746114.2789
54.8578-4.40841.10589.4756-1.50147.17240.02370.21110.68-0.67260.17250.0352-0.6956-0.414-0.18010.4119-0.0066-0.02920.22950.05190.463120.187556.677811.4077
65.51264.8724-4.1734.241-6.09899.25290.0927-0.43270.27320.3153-0.13740.0141-0.4234-0.01690.01990.22810.03610.01550.1731-0.07330.28275.831429.779741.0467
74.3757.1393-3.87022.0623-6.02564.6629-0.2120.4077-0.1086-0.42170.44020.01670.072-0.4821-0.18650.22920.0182-0.0070.2458-0.05520.31066.807135.1328.8418
88.6734-1.6712-0.56417.03570.69620.4332-0.1766-0.52960.01720.31690.1097-0.36020.34580.1032-0.07540.21750.0319-0.00810.1883-0.03380.09276.825519.969236.2626
94.74521.0718-0.10863.66593.79042.1482-0.1004-0.3044-0.54250.5002-0.22540.23021.5339-0.50550.27290.2925-0.0031-0.00090.1903-0.00990.27774.381613.969435.1835
102.1035-3.1508-6.9722.12787.88752.1351-0.36740.9034-0.53350.2662-0.4051.72990.5146-1.52670.68940.3352-0.06540.03140.4704-0.02810.4134-5.62620.037538.4385
114.9705-0.9914-3.63496.2969-2.98884.9475-0.26140.5209-0.7552-0.8719-0.41931.67090.0286-1.49740.62480.25470.0454-0.0680.5178-0.09210.5767-6.584726.559232.979
123.50810.66353.29911.3996-1.94587.5471-0.0153-0.60580.51470.72650.010.2222-0.8045-0.7837-0.01250.49320.05920.07610.3705-0.12330.24610.232831.821351.582
137.61541.0096-5.35861.6104-2.8117.26540.402-1.00290.21570.4851-0.2868-0.0747-0.71031.3442-0.03650.2976-0.0084-0.01460.2419-0.05410.16913.822225.283342.3582
143.236-0.2297-0.05099.645-2.69913.396-0.072-0.2616-0.24470.45020.21660.75430.43050.2554-0.04140.30290.04930.01870.1866-0.04710.152913.447516.355930.2439
152.15251.3711-1.50155.1036-3.56514.7099-0.35870.0196-0.3828-0.24480.0547-0.39620.82430.25360.31360.34460.02220.07890.2207-0.08970.267516.456612.877922.242
165.1156-1.4711-1.40666.7488-1.62042.12390.02520.0715-0.56290.2893-0.1028-0.73510.36761.6648-0.0110.23650.0965-0.03630.2505-0.08390.403422.91118.553629.5024
174.33130.26870.48968.41033.4837.2208-0.33370.55650.5151-0.6059-0.20690.0225-0.86180.32720.50410.3705-0.1365-0.16240.42140.16470.331614.163654.691752.4247
186.16960.97592.31260.23340.11921.4552-0.3714-0.90840.86261.9747-0.0737-1.3064-2.11650.19640.27070.7196-0.2587-0.39210.51840.0860.933315.536462.500668.2645
1910.2767-3.2377-6.63795.03131.76624.8517-0.1905-0.93780.4124-0.01960.1911-0.4562-0.18030.82250.040.2524-0.0625-0.12610.4180.05060.29919.759248.43471.7292
203.6579-4.0030.68125.73811.76645.0876-0.1040.10290.36290.1443-0.1338-0.0437-0.22930.15880.21420.2341-0.1015-0.0490.23170.07430.312812.15555.08660.3896
216.1972.8285-0.19366.8443-0.29955.8547-0.12420.47070.2094-0.3364-0.01140.03910.34380.07870.12930.21630.01820.00720.20.00470.14969.998941.610959.4449
227.5349-5.11133.91167.9009-3.53626.2224-0.4661-0.06660.8868-1.0765-0.4418-0.8518-0.57651.00310.78010.4773-0.1904-0.19490.61540.34450.732618.356761.411953.1441
239.90382.6881-0.15565.37384.29767.5730.69250.31510.51430.8374-1.2433-1.0693-1.6869-0.07590.49770.9737-0.1652-0.33560.36690.24180.6697.892271.251852.6154
245.87170.1601-2.1494.3419-0.43765.21760.179-0.9718-0.0924-0.0045-0.0789-0.41290.9123-0.0901-0.22430.7629-0.1266-0.33280.67740.17320.606910.932464.600648.4908
253.65544.4066-4.34628.4782-5.66957.5109-0.18580.15930.09060.03520.25870.1142-0.2805-0.5855-0.01920.16720.0294-0.07150.3956-0.11230.2876-3.000743.885780.8181
265.15-3.597-1.3145.7751.29724.0676-0.3083-0.0692-0.56590.260.08970.76480.6007-0.81710.21060.3144-0.1396-0.00770.44750.01480.2771-8.221632.00581.6211
273.9075-2.18052.08842.7844-3.03545.8937-0.13150.24140.10310.2313-0.18480.44680.1114-1.22330.33850.28080.00130.03450.5088-0.1340.3622-11.080842.542585.0813
281.9386-2.2619-2.74792.56531.45737.2179-0.2406-0.2053-0.06060.31960.1616-0.25990.88940.30340.1090.328-0.0158-0.04760.27430.0030.16135.541829.258575.9739
299.7619-0.5371-0.40064.8048-2.45699.2125-0.2016-0.7953-0.03820.36220.1654-0.70190.03040.81240.26830.270.0324-0.03280.2827-0.00140.220613.535129.852974.3254
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 56 )
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 95 )
3X-RAY DIFFRACTION3chain 'A' and (resid 96 through 162 )
4X-RAY DIFFRACTION4chain 'A' and (resid 163 through 201 )
5X-RAY DIFFRACTION5chain 'A' and (resid 202 through 243 )
6X-RAY DIFFRACTION6chain 'B' and (resid 0 through 21 )
7X-RAY DIFFRACTION7chain 'B' and (resid 22 through 31 )
8X-RAY DIFFRACTION8chain 'B' and (resid 32 through 45 )
9X-RAY DIFFRACTION9chain 'B' and (resid 46 through 62 )
10X-RAY DIFFRACTION10chain 'B' and (resid 63 through 72 )
11X-RAY DIFFRACTION11chain 'B' and (resid 73 through 96 )
12X-RAY DIFFRACTION12chain 'B' and (resid 97 through 112 )
13X-RAY DIFFRACTION13chain 'B' and (resid 113 through 132 )
14X-RAY DIFFRACTION14chain 'B' and (resid 133 through 148 )
15X-RAY DIFFRACTION15chain 'B' and (resid 149 through 173 )
16X-RAY DIFFRACTION16chain 'B' and (resid 174 through 187 )
17X-RAY DIFFRACTION17chain 'C' and (resid 21 through 56 )
18X-RAY DIFFRACTION18chain 'C' and (resid 57 through 73 )
19X-RAY DIFFRACTION19chain 'C' and (resid 74 through 95 )
20X-RAY DIFFRACTION20chain 'C' and (resid 96 through 147 )
21X-RAY DIFFRACTION21chain 'C' and (resid 148 through 201 )
22X-RAY DIFFRACTION22chain 'C' and (resid 202 through 213 )
23X-RAY DIFFRACTION23chain 'C' and (resid 214 through 227 )
24X-RAY DIFFRACTION24chain 'C' and (resid 228 through 241 )
25X-RAY DIFFRACTION25chain 'D' and (resid 0 through 31 )
26X-RAY DIFFRACTION26chain 'D' and (resid 32 through 82 )
27X-RAY DIFFRACTION27chain 'D' and (resid 83 through 112 )
28X-RAY DIFFRACTION28chain 'D' and (resid 113 through 173 )
29X-RAY DIFFRACTION29chain 'D' and (resid 174 through 187 )

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