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

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Basic information

Entry
Database: PDB / ID: 5wzf
TitleCrystal structure of Mycobacterium tuberculosis VapC20 (Rv2549c), Sarcin-Ricin loop cleaving toxin
Components(23S rRNA-specific endonuclease VapC20) x 2
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 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 1.2Mar 1, 2023Group: Database references / Source and taxonomy
Category: database_2 / entity_src_gen ...database_2 / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
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_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.3Oct 23, 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)32,1622
Polymers32,1622
Non-polymers00
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-10 kcal/mol
Surface area11650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.810, 59.140, 79.290
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: 16072.963 Da / Num. of mol.: 1
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: Protein 23S rRNA-specific endonuclease VapC20 / Ribonuclease VapC20 / RNase VapC20 / Toxin VapC20


Mass: 16088.963 Da / Num. of mol.: 1
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 1.78 Å3/Da / Density % sol: 30.86 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→79.29 Å / Num. all: 23389 / Num. obs: 23389 / % possible obs: 98.5 % / Redundancy: 4.3 % / Rpim(I) all: 0.035 / Rrim(I) all: 0.075 / Rsym value: 0.066 / Net I/av σ(I): 8.1 / Net I/σ(I): 11.8 / Num. measured all: 100456
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.75-1.8440.5261.41287232380.2940.6050.5262.595.6
1.84-1.9640.3472.11259431820.1940.3990.3473.898.5
1.96-2.094.10.2053.51250730300.1130.2350.2056.199.6
2.09-2.264.30.1355.41238728560.0710.1530.1358.8100
2.26-2.474.50.09971174826340.0520.1130.09911.599.8
2.47-2.774.50.0719.31075323740.0360.080.07114.699.7
2.77-3.24.50.06110.1960221140.0310.0690.06119.199.2
3.2-3.914.60.04812.7812017730.0240.0540.04825.698.3
3.91-5.534.60.0320.3640914000.0150.0330.0328.297.4
5.53-34.0074.40.03312.434647880.0170.0370.03327.194.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.95 Å34.01 Å
Translation5.95 Å34.01 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLM3.3.22data collection
SCALA3.3.22data scaling
PHASER2.5.7phasing
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→34.007 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1976 1166 4.99 %
Rwork0.1712 22184 -
obs0.1725 23350 98.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.53 Å2 / Biso mean: 25.9258 Å2 / Biso min: 10.26 Å2
Refinement stepCycle: final / Resolution: 1.75→34.007 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2048 0 0 261 2309
Biso mean---35.83 -
Num. residues----261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032124
X-RAY DIFFRACTIONf_angle_d0.7082887
X-RAY DIFFRACTIONf_chiral_restr0.027313
X-RAY DIFFRACTIONf_plane_restr0.003372
X-RAY DIFFRACTIONf_dihedral_angle_d13.013737
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 (%)
1.75-1.82970.3171620.27622597275995
1.8297-1.92610.26461350.22572718285398
1.9261-2.04680.2311480.19562763291199
2.0468-2.20480.24621630.181327882951100
2.2048-2.42660.19131520.174927822934100
2.4266-2.77760.20691420.1722817295999
2.7776-3.4990.1811260.16382842296898
3.499-34.01290.15191380.14472877301596
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)
15.58930.76170.50363.1969-0.6533.2358-0.09190.14480.1992-0.19670.0146-0.1509-0.24150.15670.05170.1725-0.00770.01850.12830.00320.114119.09056.68585.4846
21.6331-0.476-0.08232.22030.39896.677-0.0732-0.2479-0.12690.16640.1628-0.13260.65780.5795-0.1360.11760.02250.00330.19470.01690.155120.5609-3.693100.8346
38.3431-0.2697-2.63255.11223.5117.7070.083-0.35360.43320.1599-0.0452-0.1656-0.15980.2724-0.07940.1312-0.0204-0.01270.18740.03170.164823.07843.5598102.9581
45.9452.3672-0.76075.1807-3.3499.44340.1137-0.04510.60020.01020.1911-0.0226-0.58490.2004-0.26710.1437-0.03180.00720.1882-0.01250.198829.72598.445894.8453
57.12111.91454.21187.92374.93147.37650.0375-0.04790.06480.43670.08830.05090.3076-0.1024-0.10930.12060.01290.03630.16660.01050.1206-1.16781.3837106.0805
67.6271-5.9624-0.70138.7341-2.24785.0291-0.2931-0.32240.87160.11530.5034-0.7951-0.540.0317-0.20370.24410.0193-0.01860.1644-0.06710.2955-0.466313.1484110.5889
78.90795.34571.11078.62770.5394.707-0.094-0.3816-0.16670.5218-0.1170.86520.429-0.76370.22690.26240.00470.07320.34580.00450.2167-6.86342.8829113.2712
86.85423.66410.21248.28752.68375.2274-0.10530.14450.2956-0.1370.2409-0.0378-0.13610.0826-0.11230.08690.0374-0.01050.15820.02030.11057.54194.0057104.8789
95.43421.6261-0.35768.1239-1.65555.4395-0.001-0.61970.18560.44350.07150.4446-0.0428-0.0799-0.11530.19550.00840.02590.2875-0.01110.166911.59182.8698113.4245
106.4644-3.4236-5.29232.50473.01014.7173-0.3948-0.2409-0.21490.46150.16990.20870.8286-0.28350.31860.28540.01840.0260.1875-0.00250.20465.5416-9.1696105.864
116.8557-3.27150.7324.9548-5.53728.4939-0.00840.2362-0.474-0.64270.13070.36030.5255-0.3134-0.15220.1473-0.0401-0.00630.1752-0.05370.17235.437-5.288186.7176
126.6659-0.86554.00915.8634-2.14197.5321-0.28670.46720.9442-0.14070.20720.8717-0.4889-0.40060.21040.19630.0493-0.02430.28460.06430.352-1.03575.469386.278
137.54240.1508-3.95984.59690.38626.823-0.2239-0.006-0.3815-0.0980.04820.17110.3555-0.23730.15830.0988-0.0136-0.01360.1714-0.0160.1498-1.5387-4.466596.9111
148.5288-0.774-3.14918.02970.56476.3601-0.0603-0.0540.32960.00960.0590.2961-0.391-0.2434-0.00450.10990.0014-0.02520.2892-0.0040.1774-7.70433.921498.8293
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 65 )A1 - 65
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 88 )A66 - 88
3X-RAY DIFFRACTION3chain 'A' and (resid 89 through 108 )A89 - 108
4X-RAY DIFFRACTION4chain 'A' and (resid 109 through 130 )A109 - 130
5X-RAY DIFFRACTION5chain 'B' and (resid 0 through 12 )B0 - 12
6X-RAY DIFFRACTION6chain 'B' and (resid 13 through 19 )B13 - 19
7X-RAY DIFFRACTION7chain 'B' and (resid 20 through 32 )B20 - 32
8X-RAY DIFFRACTION8chain 'B' and (resid 33 through 51 )B33 - 51
9X-RAY DIFFRACTION9chain 'B' and (resid 53 through 65 )B53 - 65
10X-RAY DIFFRACTION10chain 'B' and (resid 66 through 75 )B66 - 75
11X-RAY DIFFRACTION11chain 'B' and (resid 76 through 88 )B76 - 88
12X-RAY DIFFRACTION12chain 'B' and (resid 89 through 95 )B89 - 95
13X-RAY DIFFRACTION13chain 'B' and (resid 96 through 114 )B96 - 114
14X-RAY DIFFRACTION14chain 'B' and (resid 115 through 130 )B115 - 130

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