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- PDB-5wz4: Crystal structure of Mycobacterium tuberculosis VapC20 (Rv2549c),... -

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Basic information

Entry
Database: PDB / ID: 5wz4
TitleCrystal structure of Mycobacterium tuberculosis VapC20 (Rv2549c), Sarcin-Ricin loop cleaving toxin
Components23S rRNA-specific endonuclease VapC20
KeywordsHYDROLASE / VapC toxin / Toxin-antitoxin system / Sarcin-Ricin loop cleaving toxin / Pin-domain / Homodimer
Function / homology
Function and homology information


symbiont-mediated perturbation of host process / rRNA catabolic process / RNA endonuclease activity / Hydrolases; Acting on ester bonds / magnesium ion binding
Similarity search - Function
Endonuclease VapC20 / PIN domain / VapC family / PIN domain / PIN-like domain superfamily
Similarity search - Domain/homology
23S rRNA-specific endonuclease VapC20 / 23S rRNA-specific endonuclease VapC20
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.775 Å
AuthorsThakur, K.G. / Deep, A.
Funding support India, 2items
OrganizationGrant numberCountry
Council of Scientific and Industrial Research India
Department of Science and Technology India
CitationJournal: FEBS J. / Year: 2017
Title: Crystal structure of Mycobacterium tuberculosis VapC20 toxin and its interactions with cognate antitoxin, VapB20, suggest a model for toxin-antitoxin assembly.
Authors: Deep, A. / Kaundal, S. / Agarwal, S. / Singh, R. / Thakur, K.G.
History
DepositionJan 17, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Apr 11, 2018Group: Data collection / Database references / Source and taxonomy
Category: entity_src_gen / struct_ref ...entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene ..._entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.3Mar 1, 2023Group: Database references / Source and taxonomy / Category: database_2 / entity_src_gen
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 23S rRNA-specific endonuclease VapC20
B: 23S rRNA-specific endonuclease VapC20


Theoretical massNumber of molelcules
Total (without water)32,3712
Polymers32,3712
Non-polymers00
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-11 kcal/mol
Surface area11580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.820, 59.280, 78.620
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 23S rRNA-specific endonuclease VapC20 / Ribonuclease VapC20 / RNase VapC20 / Toxin VapC20


Mass: 16185.639 Da / Num. of mol.: 2 / Mutation: D5A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: vapC20, Rv2549c / Production host: Escherichia coli (E. coli)
References: UniProt: P95004, UniProt: P0DMV7*PLUS, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.77 Å3/Da / Density % sol: 30.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Potassium thiocyanate, 30% w/v Polyethylene glycol monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97885 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97885 Å / Relative weight: 1
ReflectionResolution: 1.775→78.62 Å / Num. all: 22721 / Num. obs: 22721 / % possible obs: 99.9 % / Redundancy: 4.3 % / Rpim(I) all: 0.06 / Rrim(I) all: 0.128 / Rsym value: 0.092 / Net I/av σ(I): 6.3 / Net I/σ(I): 7.5 / Num. measured all: 98358
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
1.78-1.874.30.6011.10.3830.8020.601100
1.87-1.984.40.3951.80.250.5270.395100
1.98-2.124.40.24830.1560.330.248100
2.12-2.294.40.1594.30.1020.2150.159100
2.29-2.514.40.1245.60.0810.1720.124100
2.51-2.814.40.0848.50.0580.1230.084100
2.81-3.244.40.0611.20.0410.0870.06100
3.24-3.974.30.0619.20.0380.0810.061100
3.97-5.614.20.04911.70.0330.0690.049100
5.61-18.3243.80.03116.10.0260.0550.03197.2

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
MOSFLM0.5.8data collection
SCALA3.3.22data scaling
SOLVEphasing
RESOLVEphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.775→18.317 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 20.2
RfactorNum. reflection% reflection
Rfree0.212 1058 4.93 %
Rwork0.1747 --
obs0.1765 21466 94.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 69.32 Å2 / Biso mean: 17.5618 Å2 / Biso min: 3.17 Å2
Refinement stepCycle: final / Resolution: 1.775→18.317 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2038 0 0 272 2310
Biso mean---28.61 -
Num. residues----260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032123
X-RAY DIFFRACTIONf_angle_d0.6832889
X-RAY DIFFRACTIONf_chiral_restr0.032314
X-RAY DIFFRACTIONf_plane_restr0.003371
X-RAY DIFFRACTIONf_dihedral_angle_d15.392741
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.775-1.85570.32031250.28412238236385
1.8557-1.95350.2841320.23992330246288
1.9535-2.07570.25131290.19362496262594
2.0757-2.23570.23241390.17342546268596
2.2357-2.46020.21351200.16962622274297
2.4602-2.81510.19811300.17322652278298
2.8151-3.54250.211300.16182697282799
3.5425-18.31750.16121530.1452827298099
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)
1-0-0.00150.00040.00610.00430.0003-0.0306-0.0470.05290.03710.0385-0.0189-0.0704-0.10680.00980.15050.0514-0.02030.1447-0.01140.117322.001340.911871.437
20.14580.07270.00990.0541-0.04720.2362-0.0412-0.0262-0.04430.09910.04130.00640.176-0.07920.08360.0949-0.01710.03610.08070.00320.08422.437426.391267.8455
30.020.00030.00610.00060.00180.0025-0.0019-0.02080.0053-0.012-0.0223-0.0418-0.00460.0034-0.00480.04250.00280.0120.0814-0.01230.056834.597933.521564.7003
40.017-0.00680.04110.018-0.03740.13050.0343-0.15490.13390.08160.09460.04660.0276-0.02690.04210.1062-0.00730.03360.132-0.05660.141835.248238.210569.773
50.01390.01580.00430.0068-0.00520.01-0.0161-0.0218-0.13250.0947-0.0256-0.03580.0276-0.004100.1494-0.00240.00580.1065-0.00240.104431.686220.599665.031
60.0071-0.0060.00160.00560.00240.0040.01380.0626-0.0606-0.06380.09970.0660.0373-0.01660.01740.078-0.0152-0.00230.0904-0.01810.064129.89924.947646.8231
70.0298-0.00820.02330.0068-0.01760.0291-0.02920.1920.1338-0.0378-0.03590.1238-0.0292-0.0856-0.01110.05520.0155-0.01490.09140.00740.096225.559432.382448.2131
80.0318-0.02790.01460.0354-0.00380.0141-0.0040.0113-0.07860.03720.04430.06280.0392-0.0730.0191-0.1544-0.1340.06690.02160.01230.077223.42222.930455.1275
90.03210.00470.03160.01810.03110.0658-0.0496-0.0497-0.0788-0.005-0.03120.0463-0.05150.0291-0.00990.0548-0.01320.0080.1171-0.00250.102418.875829.495859.8465
100.00630.00750.00040.00670.00250.020.00630.05140.01690.04490.03040.0078-0.0346-0.0190.00220.03670.02520.00290.2406-0.0090.090114.790931.815658.803
110.0279-0.01470.03520.0111-0.02560.0619-0.18520.11490.141-0.0620.0177-0.1012-0.13360.1404-0.00510.1712-0.0463-0.00040.05240.01780.130549.826441.587442.2845
120.00390.0041-0.00950.0366-0.01140.05340.03790.0288-0.05330.0038-0.0059-0.04990.14360.08330.01170.07970.00490.00110.02920.01120.046844.483329.291950.5228
130.10260.06760.01670.05750.01160.0201-0.06570.12250.0939-0.06560.1173-0.0324-0.1371-0.07890.0070.08570.0401-0.01940.05130.00530.066834.302237.148544.3022
140.0453-0.0122-0.0050.02550.02610.0396-0.0452-0.0682-0.10610.0299-0.0075-0.0920.14940.0561-0.00730.1051-0.00060.02040.10920.00670.062944.218425.139957.4065
150.02140.0150.01390.01520.01020.02740.021-0.14750.15860.02250.0268-0.02160.00660.05870.00070.067-0.0165-0.00330.1251-0.08440.120545.610736.352665.7301
160.03430.0011-0.02370.0598-0.00620.0915-0.0734-0.024-0.0220.0450.03760.0174-0.05430.0209-0.0510.0361-0.0066-0.00930.0265-0.02190.062553.393334.550356.1875
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 24 )A13 - 24
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 40 )A25 - 40
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 45 )A41 - 45
4X-RAY DIFFRACTION4chain 'A' and (resid 46 through 63 )A46 - 63
5X-RAY DIFFRACTION5chain 'A' and (resid 64 through 77 )A64 - 77
6X-RAY DIFFRACTION6chain 'A' and (resid 78 through 87 )A78 - 87
7X-RAY DIFFRACTION7chain 'A' and (resid 88 through 100 )A88 - 100
8X-RAY DIFFRACTION8chain 'A' and (resid 101 through 107 )A101 - 107
9X-RAY DIFFRACTION9chain 'A' and (resid 108 through 120 )A108 - 120
10X-RAY DIFFRACTION10chain 'A' and (resid 121 through 130 )A121 - 130
11X-RAY DIFFRACTION11chain 'B' and (resid 12 through 31 )B12 - 31
12X-RAY DIFFRACTION12chain 'B' and (resid 32 through 44 )B32 - 44
13X-RAY DIFFRACTION13chain 'B' and (resid 45 through 63 )B45 - 63
14X-RAY DIFFRACTION14chain 'B' and (resid 64 through 87 )B64 - 87
15X-RAY DIFFRACTION15chain 'B' and (resid 88 through 100 )B88 - 100
16X-RAY DIFFRACTION16chain 'B' and (resid 101 through 130 )B101 - 130

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