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- PDB-5uct: Mycobacterium tuberculosis toxin MazF-mt6 -

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Basic information

Entry
Database: PDB / ID: 5uct
TitleMycobacterium tuberculosis toxin MazF-mt6
ComponentsEndoribonuclease MazF3
KeywordsHYDROLASE / toxin / Rnase / tuberculosis
Function / homology
Function and homology information


symbiont-mediated perturbation of host process / positive regulation of growth / negative regulation of growth / rRNA catabolic process / mRNA catabolic process / RNA endonuclease activity / Hydrolases; Acting on ester bonds / negative regulation of translation / negative regulation of DNA-templated transcription / DNA binding
Similarity search - Function
SH3 type barrels. - #110 / mRNA interferase PemK-like / PemK-like, MazF-like toxin of type II toxin-antitoxin system / Plasmid maintenance toxin/Cell growth inhibitor / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Endoribonuclease MazF3
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHoffer, E.H. / Dunham, C.M.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: The structure and function of Mycobacterium tuberculosis MazF-mt6 toxin provide insights into conserved features of MazF endonucleases.
Authors: Hoffer, E.D. / Miles, S.J. / Dunham, C.M.
History
DepositionDec 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2May 24, 2017Group: Database references
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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: 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: Endoribonuclease MazF3
B: Endoribonuclease MazF3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3104
Polymers22,1172
Non-polymers1922
Water1,15364
1
A: Endoribonuclease MazF3
hetero molecules

A: Endoribonuclease MazF3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3104
Polymers22,1172
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
Buried area2560 Å2
ΔGint-23 kcal/mol
Surface area9770 Å2
MethodPISA
2
B: Endoribonuclease MazF3
hetero molecules

B: Endoribonuclease MazF3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3104
Polymers22,1172
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z1
Buried area2520 Å2
ΔGint-31 kcal/mol
Surface area9730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.220, 105.220, 144.440
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z
#9: y,x,-z+1/3
#10: -y,-x,-z+1/3
#11: -x+y,y,-z
#12: x,x-y,-z+2/3
Components on special symmetry positions
IDModelComponents
11B-325-

HOH

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Components

#1: Protein Endoribonuclease MazF3 / 23S rRNA endonuclease MazF3 / Toxin MazF3 / mRNA interferase MazF-mt6


Mass: 11058.699 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: mazF3, mazF-mt6, Rv1102c / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3)
References: UniProt: P9WIH9, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 5.32 Å3/Da / Density % sol: 76.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50 mM sodium cacodylate pH 6.0, 10 mM magnesium chloride, 1.05 M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 20, 2015
RadiationMonochromator: Kohzu HLD8-24 monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→49 Å / Num. obs: 13353 / % possible obs: 98 % / Redundancy: 6.5 % / Net I/σ(I): 12

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
DIALSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4mdx

4mdx


Resolution: 2.7→49.433 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2551 681 5.1 %
Rwork0.2391 --
obs0.2401 13352 98.43 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→49.433 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1514 0 0 64 1578
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031538
X-RAY DIFFRACTIONf_angle_d0.552116
X-RAY DIFFRACTIONf_dihedral_angle_d12.947938
X-RAY DIFFRACTIONf_chiral_restr0.047267
X-RAY DIFFRACTIONf_plane_restr0.005275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.90840.351360.35482470X-RAY DIFFRACTION99
2.9084-3.20110.36061360.32192505X-RAY DIFFRACTION99
3.2011-3.66420.27111380.27072496X-RAY DIFFRACTION99
3.6642-4.61590.26241330.21312540X-RAY DIFFRACTION98
4.6159-49.44130.21581380.21892660X-RAY DIFFRACTION97
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)
17.0437-0.49891.93942.1879-3.96397.83-0.8144-0.14030.31020.12230.70232.1332-1.099-0.23650.07010.8483-0.047-0.03170.52350.17541.008343.56186.513320.0308
22.1260.79011.24583.75840.25953.0826-0.4194-0.0951-0.8021-0.18830.63291.13150.9499-0.0953-0.32040.9253-0.07520.13860.49870.18840.869343.8262-5.911121.6302
33.5262.3383-1.38312.0394-2.14314.8254-0.66750.3234-0.23420.48041.1332.42550.2381-0.8163-0.1880.8725-0.08980.28730.58390.24441.312240.2219-2.509421.2783
46.3651-0.9132-2.1352.88342.96825.2853-1.2248-0.1146-0.12990.22620.00651.399-0.052-0.85590.9470.98750.06680.27160.66580.041.720435.42837.341919.4864
50.150.09780.51870.12590.26821.98470.05870.5382-0.0520.3853-0.28570.4117-0.4316-1.37040.31872.20730.67282.10141.029-0.25120.997537.90080.882233.7878
60.4632-1.6403-0.19548.87713.41442.48490.2951-0.5949-0.6751.03350.2702-0.13981.49090.5841-0.27891.89920.12680.0480.45210.22970.547951.6894-4.333833.3332
77.7069-3.6816-1.72071.81070.77455.62480.57830.24960.27180.9745-0.75310.4331-0.128-0.34490.19850.7095-0.19950.04160.52480.02280.402949.5255-23.935612.3118
84.3692.1914.19462.72221.40456.2711-0.323-1.29551.42120.5299-0.3593-0.8580.67231.15960.31390.99830.0846-0.11710.7474-0.06240.90463.0101-29.20549.5556
95.2376-0.6723-4.0122.5885-0.3094.23010.44140.35950.8094-0.0384-0.12270.1935-0.0978-0.3918-0.3680.6144-0.03990.02750.39690.06810.517743.7343-27.525.6449
105.35450.2324-1.49192.8858-1.99891.86950.7729-0.1335-0.03250.55970.12640.2221-0.4311-0.8377-0.50230.8472-0.26620.09070.53210.06690.478841.2549-29.993411.8701
116.45844.3778-3.04536.23291.06744.57550.8767-1.48950.01610.8606-0.6734-0.3793-0.19621.1882-0.31140.8226-0.16760.06170.70240.01380.434353.2118-24.487312.86
127.3643-3.41470.29566.0503-0.82920.1273-0.26530.7155-1.2473-0.2448-0.05380.62941.1943-0.4750.08430.7368-0.0759-0.00680.39430.02990.759248.0748-39.43262.3055
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 28 )
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 44 )
3X-RAY DIFFRACTION3chain 'A' and (resid 45 through 72 )
4X-RAY DIFFRACTION4chain 'A' and (resid 73 through 79 )
5X-RAY DIFFRACTION5chain 'A' and (resid 80 through 86 )
6X-RAY DIFFRACTION6chain 'A' and (resid 87 through 100 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 17 )
8X-RAY DIFFRACTION8chain 'B' and (resid 18 through 28 )
9X-RAY DIFFRACTION9chain 'B' and (resid 29 through 44 )
10X-RAY DIFFRACTION10chain 'B' and (resid 45 through 64 )
11X-RAY DIFFRACTION11chain 'B' and (resid 65 through 81 )
12X-RAY DIFFRACTION12chain 'B' and (resid 82 through 100 )

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