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- PDB-6a7v: Crystal structure of Mycobacterium tuberculosis VapBC11 toxin-ant... -

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Basic information

Entry
Database: PDB / ID: 6a7v
TitleCrystal structure of Mycobacterium tuberculosis VapBC11 toxin-antitoxin complex
Components
  • Antitoxin VapB11
  • Ribonuclease VapC11
KeywordsTOXIN/ANTITOXIN / VapBC / Endoribonuclease / tRNase / Rv1560-Rv1561 / TOXIN / TOXIN-ANTITOXIN complex
Function / homology
Function and homology information


response to host / positive regulation of growth / toxin sequestering activity / negative regulation of growth / RNA nuclease activity / positive regulation of translation / negative regulation of translation / Hydrolases; Acting on ester bonds / magnesium ion binding
Similarity search - Function
Bacterial antitoxin of type II TA system, VapB / Bacterial antitoxin of type II TA system, VapB / PIN domain / VapC family / PIN domain / PIN-like domain superfamily
Similarity search - Domain/homology
Ribonuclease VapC11 / Antitoxin VapB11
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsDeep, A. / Thakur, K.G.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research India
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Structural, functional and biological insights into the role of Mycobacterium tuberculosis VapBC11 toxin-antitoxin system: targeting a tRNase to tackle mycobacterial adaptation.
Authors: Deep, A. / Tiwari, P. / Agarwal, S. / Kaundal, S. / Kidwai, S. / Singh, R. / Thakur, K.G.
History
DepositionJul 4, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
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 / _entity.formula_weight
Revision 1.2Nov 22, 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: Ribonuclease VapC11
K: Antitoxin VapB11
C: Ribonuclease VapC11
D: Antitoxin VapB11
E: Ribonuclease VapC11
U: Antitoxin VapB11
G: Ribonuclease VapC11
H: Antitoxin VapB11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,00711
Polymers88,5768
Non-polymers4303
Water10,395577
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Formation of Heterooctameric complex was also confirmed by Analytical ultracentrifugation.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26820 Å2
ΔGint-130 kcal/mol
Surface area29060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.555, 127.007, 151.207
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Ribonuclease VapC11 / RNase VapC11 / Toxin VapC11


Mass: 15248.295 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: vapC11, Rv1561, MTCY48.04c / Production host: Escherichia coli (E. coli)
References: UniProt: P9WFA5, Hydrolases; Acting on ester bonds
#2: Protein
Antitoxin VapB11


Mass: 6895.794 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: vapB11, Rv1560, MTCY48.05c / Production host: Escherichia coli (E. coli) / References: UniProt: P9WLU3
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 577 / 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: 2.77 Å3/Da / Density % sol: 55.67 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6.5
Details: 0.1M Ammonium Sulphate, 0.3M Sodium formate, 0.1 Sodium cacodylate, 3 % w/v PGA-LM, 30% PEG400 (pH 6.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0723 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 1.67→97.252 Å / Num. all: 113379 / Num. obs: 113379 / % possible obs: 99.7 % / Redundancy: 4.6 % / Rpim(I) all: 0.023 / Rrim(I) all: 0.05 / Rsym value: 0.044 / Net I/av σ(I): 11.5 / Net I/σ(I): 15.7 / Num. measured all: 517561
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.67-1.764.40.8810.971241161760.4610.9990.8811.498.8
1.76-1.874.70.5311.572596156060.270.5980.5312.599.9
1.87-24.50.3182.465838145870.1660.360.3184.299.9
2-2.164.70.1624.764599136310.0830.1830.1627.999.9
2.16-2.364.50.17.556245125780.0530.1130.112.299.8
2.36-2.644.80.06311.554657114510.0320.0710.06318.699.9
2.64-3.054.50.04116.945547101000.0220.0470.04126.999.7
3.05-3.734.70.02823.24056386160.0140.0310.02842.399.8
3.73-5.284.40.02327.12968867470.0120.0260.0235199.6
5.28-47.9464.30.02123.61658738870.0120.0240.02151.299.2

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Processing

Software
NameVersionClassification
REFMAC3.3.22refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CHG

4chg


Resolution: 1.67→97.25 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.499 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2086 5653 5 %RANDOM
Rwork0.183 ---
obs0.1843 107637 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 134.27 Å2 / Biso mean: 39.158 Å2 / Biso min: 9.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20 Å2
2--0.11 Å2-0 Å2
3----0.63 Å2
Refinement stepCycle: final / Resolution: 1.67→97.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6122 0 26 577 6725
Biso mean--52.3 44.17 -
Num. residues----795
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196234
X-RAY DIFFRACTIONr_bond_other_d0.0010.026024
X-RAY DIFFRACTIONr_angle_refined_deg1.2981.9598433
X-RAY DIFFRACTIONr_angle_other_deg0.78313749
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3785793
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.14621.927301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.745151051
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3151592
X-RAY DIFFRACTIONr_chiral_restr0.0910.2997
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027028
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021384
X-RAY DIFFRACTIONr_rigid_bond_restr13.195312258
X-RAY DIFFRACTIONr_sphericity_free30.735330
X-RAY DIFFRACTIONr_sphericity_bonded12.625512436
LS refinement shellResolution: 1.67→1.713 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 393 -
Rwork0.363 7697 -
all-8090 -
obs--97.43 %
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)
10.083-0.1294-0.23290.29350.23330.8491-0.05050.0034-0.01460.04310.00730.01360.1653-0.0320.04320.10660.00030.00190.00330.00110.0462-2.27760.74952.514
20.1045-0.05640.17470.6188-0.52221.10330.0307-0.0011-0.04480.01510.07410.1152-0.0943-0.1123-0.10480.10620.02050.02110.02590.00980.0584-8.73358.05581.187
30.11480.0559-0.08880.037-0.05120.6585-0.0114-0.0487-0.00560.0224-0.0279-0.01760.01820.07620.03940.1016-0.0031-0.01240.02380.00520.0562-1.11374.40273.543
40.9037-0.49690.27460.5808-0.16350.09680.01040.07020.06370.0004-0.0451-0.03620.03390.0010.03460.1091-0.02680.02860.0557-0.01740.0449-18.53579.0770.411
50.10750.0139-0.24420.1701-0.11980.62190.0214-0.00020.01030.00310.02130.001-0.0962-0.0134-0.04270.1078-0.00220.01210.00920.00140.05252.29197.5745.87
60.10580.0810.10860.2753-0.12120.3485-0.04790.02020.0343-0.06420.05920.04990.0408-0.0295-0.01130.118-0.0265-0.0160.01660.00590.0648-2.64479.4348.58
70.6073-0.11080.06350.58690.46080.57640.01660.0655-0.0884-0.13990.014-0.0699-0.04030.143-0.03060.12450.03290.02110.08710.01470.059911.98383.48327.606
82.94230.6230.30572.38330.00320.0630.1501-0.2316-0.0739-0.3367-0.15010.35-0.0347-0.0675-0.00010.18930.0902-0.07430.1176-0.03020.0651-4.93182.66321.519
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 134
2X-RAY DIFFRACTION2C201
3X-RAY DIFFRACTION3C-4 - 134
4X-RAY DIFFRACTION4D2 - 63
5X-RAY DIFFRACTION5E0 - 134
6X-RAY DIFFRACTION6A201
7X-RAY DIFFRACTION7G-3 - 134
8X-RAY DIFFRACTION8H2 - 63

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