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- PDB-6l2a: A mutant form of M. tb toxin MazEF-mt1 -

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Basic information

Entry
Database: PDB / ID: 6l2a
TitleA mutant form of M. tb toxin MazEF-mt1
ComponentsmRNA interferase
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 / hydrolase activity / 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
mRNA interferase / Endoribonuclease MazF9
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.90044665179 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
DepositionOct 3, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Nov 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

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Assembly

Deposited unit
A: mRNA interferase


Theoretical massNumber of molelcules
Total (without water)12,9981
Polymers12,9981
Non-polymers00
Water1,08160
1
A: mRNA interferase

A: mRNA interferase


Theoretical massNumber of molelcules
Total (without water)25,9962
Polymers25,9962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area1700 Å2
ΔGint-11 kcal/mol
Surface area10950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.313, 42.313, 87.612
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein mRNA interferase


Mass: 12997.886 Da / Num. of mol.: 1 / Mutation: D11S,P14A,S18A,D13G,E89A,R90A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: mazF9 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0E7Y7J2, UniProt: P71650*PLUS, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 1.74 Å3/Da / Density % sol: 29.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 20% poly (ethylene glycol) 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: SEALED TUBE / Type: OXFORD DIFFRACTION SUPERNOVA / Wavelength: 1.54 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Sep 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→21.9 Å / Num. obs: 7614 / % possible obs: 99.9 % / Redundancy: 8.3 % / Biso Wilson estimate: 21.7376684597 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.089 / Net I/σ(I): 17
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.973 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1086 / CC1/2: 0.669

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KYS

6kys


Resolution: 1.90044665179→20.5652061793 Å / SU ML: 0.13023928667 / Cross valid method: FREE R-VALUE / σ(F): 1.33792440413 / Phase error: 24.859918438
RfactorNum. reflection% reflection
Rfree0.232803375054 379 4.9973628692 %
Rwork0.19695247723 --
obs0.19884316004 7584 99.9736356446 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 26.5825143967 Å2
Refinement stepCycle: LAST / Resolution: 1.90044665179→20.5652061793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms821 0 0 62 883
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00293694671018831
X-RAY DIFFRACTIONf_angle_d0.6010480098121133
X-RAY DIFFRACTIONf_chiral_restr0.0459294277489145
X-RAY DIFFRACTIONf_plane_restr0.00277741330599142
X-RAY DIFFRACTIONf_dihedral_angle_d19.9757998935509
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.901-2.17520.2745644902031260.2157947268522329X-RAY DIFFRACTION100
2.1752-2.73950.2382891003981000.2166251570112398X-RAY DIFFRACTION100
2.7395-20.5650.22040366481530.182737080152478X-RAY DIFFRACTION100

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