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- PDB-6kyt: The structure of the M. tb toxin MazEF-mt1 complex -

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Basic information

Entry
Database: PDB / ID: 6kyt
TitleThe structure of the M. tb toxin MazEF-mt1 complex
Components
  • Antitoxin MazE9
  • Endoribonuclease MazF9
KeywordsTOXIN / RNA endonlease / protein engineering
Function / homology
Function and homology information


modulation by symbiont of host process / positive regulation of growth / toxin sequestering activity / negative regulation of growth / rRNA catabolic process / mRNA catabolic process / RNA endonuclease activity / Hydrolases; Acting on ester bonds / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Ribbon-helix-helix protein, CopG / Ribbon-helix-helix protein, copG family / 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
Antitoxin MazE9 / Endoribonuclease MazF9
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.00101167265 Å
AuthorsXie, W. / Chen, R. / Zhou, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870782 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
P: Antitoxin MazE9
D: Endoribonuclease MazF9
E: Endoribonuclease MazF9
F: Antitoxin MazE9
G: Endoribonuclease MazF9
H: Endoribonuclease MazF9
J: Endoribonuclease MazF9
K: Endoribonuclease MazF9
Q: Antitoxin MazE9
C: Antitoxin MazE9


Theoretical massNumber of molelcules
Total (without water)141,97212
Polymers141,97212
Non-polymers00
Water8,053447
1
A: Endoribonuclease MazF9
B: Endoribonuclease MazF9
P: Antitoxin MazE9
J: Endoribonuclease MazF9
K: Endoribonuclease MazF9
Q: Antitoxin MazE9


Theoretical massNumber of molelcules
Total (without water)70,9866
Polymers70,9866
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14630 Å2
ΔGint-73 kcal/mol
Surface area25280 Å2
MethodPISA
2
D: Endoribonuclease MazF9
E: Endoribonuclease MazF9
F: Antitoxin MazE9
G: Endoribonuclease MazF9
H: Endoribonuclease MazF9
C: Antitoxin MazE9


Theoretical massNumber of molelcules
Total (without water)70,9866
Polymers70,9866
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14930 Å2
ΔGint-66 kcal/mol
Surface area25900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.697, 161.140, 78.851
Angle α, β, γ (deg.)90.000, 99.628, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Endoribonuclease MazF9


Mass: 13336.267 Da / Num. of mol.: 8
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: Protein
Antitoxin MazE9


Mass: 8820.548 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: mazE9, mazE-mt1, Rv2801A / Production host: Escherichia coli (E. coli) / References: UniProt: P0CL61
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 447 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAuthors state that some bacteria start with Val instead of Met.

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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: 49.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 25% PEG1500, 0.1M BIS-Tris pH 9.0, 0.1M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 85400 / % possible obs: 99.8 % / Redundancy: 6.8 % / Biso Wilson estimate: 38.0217435608 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.076 / Net I/σ(I): 18.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.907 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 8535 / CC1/2: 0.698 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PHENIX1.10.1_2155refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WYG

5wyg


Resolution: 2.00101167265→28.6812112422 Å / SU ML: 0.25269194232 / Cross valid method: FREE R-VALUE / σ(F): 1.37389974749 / Phase error: 24.2833158338
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.229838408828 4231 4.97062969925 %
Rwork0.194544948525 80889 -
obs0.196306485999 85120 99.6569608842 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.2287304238 Å2
Refinement stepCycle: LAST / Resolution: 2.00101167265→28.6812112422 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9217 0 0 447 9664
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003011389782749344
X-RAY DIFFRACTIONf_angle_d0.63458953794412742
X-RAY DIFFRACTIONf_chiral_restr0.0441473324141539
X-RAY DIFFRACTIONf_plane_restr0.004285755318571656
X-RAY DIFFRACTIONf_dihedral_angle_d14.7096537775687
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.002-2.02370.3396924645121290.293232936612642X-RAY DIFFRACTION96.7865874956
2.0237-2.04750.3090123387711300.2714107571542680X-RAY DIFFRACTION99.7161107168
2.0475-2.07250.3204994867011340.2737896932672737X-RAY DIFFRACTION99.7567755386
2.0725-2.09870.3087616892141260.2550989634272654X-RAY DIFFRACTION100
2.0987-2.12630.2974309337881480.2466249824112707X-RAY DIFFRACTION99.9299964998
2.1263-2.15550.2552900511191470.2347637142762736X-RAY DIFFRACTION99.896049896
2.1555-2.18620.2729017565371520.234595365912647X-RAY DIFFRACTION100
2.1862-2.21890.2553850512491350.2340130063422693X-RAY DIFFRACTION100
2.2189-2.25350.2940645575131530.2268414908342760X-RAY DIFFRACTION99.8971193416
2.2535-2.29050.248881397951350.236542815272632X-RAY DIFFRACTION99.8916967509
2.2905-2.32990.3093453825491530.2332165669992678X-RAY DIFFRACTION99.7182106375
2.3299-2.37230.2749789721661410.2299030502152722X-RAY DIFFRACTION99.9301919721
2.3723-2.41790.2797404258261660.2227966036642657X-RAY DIFFRACTION99.9645892351
2.4179-2.46720.2614730886381430.2272058281662729X-RAY DIFFRACTION99.9651931779
2.4672-2.52080.2580211965341280.2241238119892670X-RAY DIFFRACTION99.9642729546
2.5208-2.57940.2816859131761440.2213252015462710X-RAY DIFFRACTION99.9649737303
2.5794-2.64390.2570462246141440.2078578753712706X-RAY DIFFRACTION99.9649245879
2.6439-2.71530.267668726321540.2024833448322722X-RAY DIFFRACTION99.7918112422
2.7153-2.79520.2402992062211310.2072164205682640X-RAY DIFFRACTION99.8198847262
2.7952-2.88530.2454897001841370.2102514079472740X-RAY DIFFRACTION99.4813278008
2.8853-2.98830.2522546851731490.2051339592292681X-RAY DIFFRACTION99.9293785311
2.9883-3.10780.26345311351250.2025088799462714X-RAY DIFFRACTION99.9647887324
3.1078-3.24910.2289034838361300.2040724554952718X-RAY DIFFRACTION99.9648999649
3.2491-3.42010.2368717596751530.1968757691652703X-RAY DIFFRACTION99.9300209937
3.4201-3.6340.24954472781480.189429897952676X-RAY DIFFRACTION99.6119929453
3.634-3.9140.1863866885711560.1758728581482682X-RAY DIFFRACTION99.5789473684
3.914-4.30670.1746228912061120.1613786720852761X-RAY DIFFRACTION99.8262682418
4.3067-4.92710.1852152812521490.1474937327522678X-RAY DIFFRACTION99.6475149806
4.9271-6.19730.233718434911320.1840377944622714X-RAY DIFFRACTION99.1292232672
6.1973-28.68120.1713979018681470.1699867420452700X-RAY DIFFRACTION97.8014428032

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