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- PDB-5sv2: Toxin VapC21 from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 5sv2
TitleToxin VapC21 from Mycobacterium tuberculosis
ComponentsRibonuclease VapC21
KeywordsHYDROLASE / toxin-antitoxin / VapC / VapBC / RNAse / VapC21
Function / homology
Function and homology information


negative regulation of growth / RNA nuclease activity / Hydrolases; Acting on ester bonds / magnesium ion binding
Similarity search - Function
PIN domain / VapC family / 5'-nuclease / PIN domain / PIN-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.31 Å
Model detailsVapC21, the toxin part of a Mycobacterium tuberculosis' toxin-antitoxin system
AuthorsValadares, N.F.
Funding support Brazil, 2items
OrganizationGrant numberCountry
FAPDF193.000.647/2015 Brazil
FAPDF193.001.015/2015 Brazil
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2016
Title: Crystal structure of VapC21 from Mycobacterium tuberculosis at 1.31 angstrom resolution.
Authors: Jardim, P. / Santos, I.C. / Barbosa, J.A.R.G. / de Freitas, S.M. / Valadares, N.F.
History
DepositionAug 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references
Revision 1.2Jun 21, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: citation / citation_author ...citation / citation_author / diffrn_detector / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _citation_author.name ..._citation.journal_id_CSD / _citation_author.name / _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Oct 4, 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 VapC21


Theoretical massNumber of molelcules
Total (without water)16,8251
Polymers16,8251
Non-polymers00
Water2,720151
1
A: Ribonuclease VapC21

A: Ribonuclease VapC21


Theoretical massNumber of molelcules
Total (without water)33,6502
Polymers33,6502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area2930 Å2
ΔGint-22 kcal/mol
Surface area12600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.339, 44.351, 56.530
Angle α, β, γ (deg.)90.000, 101.720, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-312-

HOH

21A-338-

HOH

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Components

#1: Protein Ribonuclease VapC21 / RNase VapC21 / Toxin VapC21


Mass: 16825.158 Da / Num. of mol.: 1 / Mutation: D8A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: vapC21, Rv2757c / Plasmid: pET24a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P9WF91, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.44 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 0.1 M Hepes pH 7.5, 8% v/v ethylene glycol, 10% w/v polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.2398 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2398 Å / Relative weight: 1
ReflectionResolution: 1.31→35.678 Å / Num. obs: 67560 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Biso Wilson estimate: 14.95 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Net I/σ(I): 22.4
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.31-1.390.3842.50.824184
1.39-1.480.1955.670.955195.3
1.48-1.60.10711.410.986198.3
1.6-1.760.07118.830.996199.2
1.76-1.960.04627.670.998199.7
1.96-2.270.03636.860.998199.6
2.27-2.770.03344.990.998199.2
2.77-3.910.03149.810.999199.7
3.91-35.6780.02953.30.999199.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H87

3h87


Resolution: 1.31→30.03 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0.97 / Phase error: 16.3
RfactorNum. reflection% reflection
Rfree0.1597 3388 5.02 %
Rwork0.1419 --
obs0.1428 67555 96.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 114.91 Å2 / Biso mean: 25.8742 Å2 / Biso min: 8.42 Å2
Refinement stepCycle: final / Resolution: 1.31→30.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1080 0 0 151 1231
Biso mean---37.98 -
Num. residues----135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081186
X-RAY DIFFRACTIONf_angle_d0.9611623
X-RAY DIFFRACTIONf_chiral_restr0.075177
X-RAY DIFFRACTIONf_plane_restr0.007214
X-RAY DIFFRACTIONf_dihedral_angle_d21.702456
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3095-1.32820.45981020.40141957205971
1.3282-1.34810.32191300.33862451258186
1.3481-1.36910.31561250.28832347247288
1.3691-1.39160.25691370.24982601273891
1.3916-1.41560.25471380.222579271794
1.4156-1.44130.22411410.19352686282797
1.4413-1.4690.21061420.17542701284397
1.469-1.4990.17831420.16132665280795
1.499-1.53160.15661440.14742731287598
1.5316-1.56720.17241460.15022762290898
1.5672-1.60640.18581430.14542692283599
1.6064-1.64990.15951450.14152804294999
1.6499-1.69840.16221430.13382749289299
1.6984-1.75320.17631470.13672740288799
1.7532-1.81590.17261460.134427762922100
1.8159-1.88860.14871470.128628022949100
1.8886-1.97450.15621430.129627362879100
1.9745-2.07860.13611460.125927582904100
2.0786-2.20880.141470.126528202967100
2.2088-2.37920.16221450.1232733287899
2.3792-2.61860.13081470.11662782292999
2.6186-2.99720.16441430.12592740288399
2.9972-3.77490.13961490.130627912940100
3.7749-30.0380.14481500.150627642914100
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)
14.3390.1312-1.78933.0897-0.52513.79750.0872-0.3436-0.0352-0.003-0.11220.15630.4947-0.33520.14370.2263-0.0205-0.01190.24980.00030.1301-3.4199-13.5273-8.4268
22.43590.0762-0.50150.77640.11030.5313-0.0482-0.07970.03870.0440.02880.10640.0406-0.03640.03850.0810.0020.00280.08030.00940.1028-2.1854-7.691-20.9187
36.0751-1.2929-1.013.99680.34433.987-0.3089-0.3368-0.35310.32530.1879-0.02070.14010.0950.04980.14170.04280.02410.110.03750.185918.9333-18.6517-22.5782
42.44010.5681-0.62871.2018-0.07411.668-0.1287-0.5467-0.15590.25330.0637-0.08620.35020.40580.04820.18570.07740.00480.23220.01770.14299.6396-11.6988-13.1046
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 29 )A2 - 29
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 83 )A30 - 83
3X-RAY DIFFRACTION3chain 'A' and (resid 84 through 94 )A84 - 94
4X-RAY DIFFRACTION4chain 'A' and (resid 95 through 136 )A95 - 136

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