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- PDB-6l29: The structure of the MazF-mt1 mutant -

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Basic information

Entry
Database: PDB / ID: 6l29
TitleThe structure of the MazF-mt1 mutant
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 / 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
mRNA interferase / Endoribonuclease MazF9
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.30000510246 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 2, 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: mRNA interferase
B: mRNA interferase


Theoretical massNumber of molelcules
Total (without water)26,4002
Polymers26,4002
Non-polymers00
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, PDBePISA
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-7 kcal/mol
Surface area10670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.644, 51.872, 129.635
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein mRNA interferase


Mass: 13200.074 Da / Num. of mol.: 2 / Mutation: D11S,P14A,S18A
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.: 138 / 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: 2.3 Å3/Da / Density % sol: 46.48 %
Crystal growTemperature: 298 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 FR-E+ DW / Wavelength: 1.54 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Jul 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→20.972 Å / Num. obs: 10906 / % possible obs: 96.9 % / Redundancy: 2.9 % / Biso Wilson estimate: 17.0324233196 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.092 / Net I/σ(I): 10.8
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 1525 / CC1/2: 0.919 / % possible all: 94.9

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Processing

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

6kys


Resolution: 2.30000510246→20.97 Å / SU ML: 0.271819547125 / Cross valid method: FREE R-VALUE / σ(F): 1.34003750718 / Phase error: 22.3349555004
RfactorNum. reflection% reflection
Rfree0.232009891394 538 4.95076838134 %
Rwork0.18218331791 --
obs0.184667275305 10867 96.4583703178 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 20.0362140365 Å2
Refinement stepCycle: LAST / Resolution: 2.30000510246→20.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1809 0 0 138 1947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004140889935841830
X-RAY DIFFRACTIONf_angle_d0.6959614193182492
X-RAY DIFFRACTIONf_chiral_restr0.0459222772755306
X-RAY DIFFRACTIONf_plane_restr0.00424882456872325
X-RAY DIFFRACTIONf_dihedral_angle_d17.92940836451126
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.53110.3188213099271220.2172104591622499X-RAY DIFFRACTION94.7920433996
2.5311-2.89660.255833189351460.2001375451562548X-RAY DIFFRACTION97.7503628447
2.8966-3.64620.2221472566761250.1717138369462653X-RAY DIFFRACTION99.0374331551
3.6462-20.970.1934128973781450.1665614983362629X-RAY DIFFRACTION94.3537414966

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