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- PDB-6kys: The structure of the M. tb toxin MazF-mt1 -

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Basic information

Entry
Database: PDB / ID: 6kys
TitleThe structure of the M. tb toxin MazF-mt1
ComponentsEndoribonuclease MazF9
KeywordsTOXIN / RNA endonlease / protein engineering
Function / homology
Function and homology information


symbiont-mediated perturbation of host process / negative regulation of growth / rRNA catabolic process / mRNA catabolic process / RNA endonuclease activity / Hydrolases; Acting on ester bonds / DNA binding
Similarity search - Function
mRNA interferase PemK-like / PemK-like, MazF-like toxin of type II toxin-antitoxin system / Plasmid maintenance toxin/Cell growth inhibitor
Similarity search - Domain/homology
Endoribonuclease MazF9
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.20041403544 Å
AuthorsXie, W. / Chen, R. / Zhou, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31870782 China
CitationJournal: Acs Infect Dis. / Year: 2020
Title: Conserved Conformational Changes in the Regulation ofMycobacterium tuberculosisMazEF-mt1.
Authors: Chen, R. / Zhou, J. / Sun, R. / Du, C. / Xie, W.
History
DepositionSep 20, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 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: Endoribonuclease MazF9
B: Endoribonuclease MazF9


Theoretical massNumber of molelcules
Total (without water)26,5402
Polymers26,5402
Non-polymers00
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, PDBe PISA
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-6 kcal/mol
Surface area10510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.140, 72.485, 60.975
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Endoribonuclease MazF9 / Toxin MazF9 / mRNA interferase MazF-mt1


Mass: 13270.121 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: mazF9, mazF-mt1, Rv2801c / Production host: Escherichia coli (E. coli)
References: UniProt: P71650, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.2 Å3/Da / Density % sol: 44.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 20% PEG 3350, 0.1 M NaOAc pH 5.0, and 0.1 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: May 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→22.46 Å / Num. obs: 12032 / % possible obs: 98.7 % / Redundancy: 4.8 % / Biso Wilson estimate: 11.7643466651 Å2 / CC1/2: 0.966 / Rmerge(I) obs: 0.25 / Net I/σ(I): 5.8
Reflection shellResolution: 2.2→2.32 Å / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1728 / CC1/2: 0.669 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
CrysalisProdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HJZ

5hjz


Resolution: 2.20041403544→22.46 Å / SU ML: 0.29594408584 / Cross valid method: FREE R-VALUE / σ(F): 0.104864264202 / Phase error: 26.4034888733
RfactorNum. reflection% reflection
Rfree0.258630012011 1111 5.01195470745 %
Rwork0.210546376617 --
obs0.212967304022 12004 97.9021287872 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 15.9374750704 Å2
Refinement stepCycle: LAST / Resolution: 2.20041403544→22.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1814 0 0 150 1964
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004606093118891835
X-RAY DIFFRACTIONf_angle_d0.7732959458782501
X-RAY DIFFRACTIONf_chiral_restr0.0501558800813307
X-RAY DIFFRACTIONf_plane_restr0.00499253390029330
X-RAY DIFFRACTIONf_dihedral_angle_d16.19089618161137
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.30050.3739364562131340.300281919312598X-RAY DIFFRACTION96.8450903935
2.3005-2.42160.3146192152911320.2451327377362689X-RAY DIFFRACTION99.5061728395
2.4216-2.57310.3055724272981390.2369981083082678X-RAY DIFFRACTION99.4001411433
2.5731-2.77150.3094953715881160.2259967591852718X-RAY DIFFRACTION99.4037179937
2.7715-3.04980.2225758822981610.2128986009592624X-RAY DIFFRACTION99.2516037063
3.0498-3.48970.2574862890761470.1997119992962640X-RAY DIFFRACTION98.5153764581
3.4897-4.39120.2179034758251350.1715263312452609X-RAY DIFFRACTION97.0640254687
4.3912-22.460.2063448685251470.1745623769612500X-RAY DIFFRACTION93.3027846317

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