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- PDB-7d2n: Crystal structure of MazE-MazF (Form-III) from Deinococcus radiodurans -

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Basic information

Entry
Database: PDB / ID: 7d2n
TitleCrystal structure of MazE-MazF (Form-III) from Deinococcus radiodurans
Components
  • AbrB/MazE/SpoVT family DNA-binding domain-containing protein
  • Endoribonuclease MazF
KeywordsTOXIN / MazEF toxin-antitoxin system / Antitoxin / endonuclease
Function / homology
Function and homology information


toxin sequestering activity / rRNA catabolic process / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / mRNA catabolic process / RNA endonuclease activity / hydrolase activity / DNA binding
Similarity search - Function
: / SpoVT / AbrB like domain / Antidote-toxin recognition MazE, bacterial antitoxin / SpoVT-AbrB domain profile. / SpoVT-AbrB domain / SpoVT-AbrB domain superfamily / 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
AbrB/MazE/SpoVT family DNA-binding domain-containing protein / Endoribonuclease MazF / PpGpp-regulated growth inhibitor ChpA/MazF, putative / PpGpp-regulated growth inhibitor suppressor ChpR/MazE, putative
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDhanasingh, I. / Lee, S.H.
CitationJournal: J.Microbiol / Year: 2021
Title: Functional and structural characterization of Deinococcus radiodurans R1 MazEF toxin-antitoxin system, Dr0416-Dr0417.
Authors: Dhanasingh, I. / Choi, E. / Lee, J. / Lee, S.H. / Hwang, J.
History
DepositionSep 17, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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 MazF
D: Endoribonuclease MazF
E: AbrB/MazE/SpoVT family DNA-binding domain-containing protein
B: Endoribonuclease MazF
C: Endoribonuclease MazF
F: AbrB/MazE/SpoVT family DNA-binding domain-containing protein


Theoretical massNumber of molelcules
Total (without water)67,6976
Polymers67,6976
Non-polymers00
Water8,323462
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.606, 56.215, 61.822
Angle α, β, γ (deg.)90.000, 107.310, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Endoribonuclease MazF


Mass: 12465.216 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: mazF, HAV23_04965, HAV35_11860 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A6G9BVQ8, UniProt: Q9RX98*PLUS, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: Protein AbrB/MazE/SpoVT family DNA-binding domain-containing protein


Mass: 8918.065 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: HAV23_04960, HAV35_11865 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6G9BVE7, UniProt: Q9RX99*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / 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: 1.7 Å3/Da / Density % sol: 27.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Sodium thiocyanate, 20% PEG 3,350, pH 6.9

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 58095 / % possible obs: 97 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.05 / Rrim(I) all: 0.099 / Χ2: 2.272 / Net I/σ(I): 7.3 / Num. measured all: 446024
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.633.90.87256210.8190.5091.011.04394.8
1.63-1.663.90.73256430.8790.4250.8461.06295.9
1.66-1.693.90.61155680.9050.3550.7061.09195.7
1.69-1.723.90.52956010.9240.3080.6131.21695.7
1.72-1.763.90.40856970.9530.2370.4721.26796
1.76-1.83.90.35255670.9640.2050.4081.31496.3
1.8-1.853.90.28156350.9720.1630.3251.45696.6
1.85-1.93.90.25456730.9780.1480.2941.59396.6
1.9-1.953.90.21556600.9820.1250.2481.72696.8
1.95-2.023.90.16757600.9870.0970.1931.93197
2.02-2.093.90.1456930.9890.0820.1622.07297.2
2.09-2.173.90.12556610.9910.0730.1452.14897.3
2.17-2.273.90.1157270.9910.0640.1282.33997.4
2.27-2.393.90.09757180.9930.0560.1122.48997.7
2.39-2.543.90.08957350.9940.0520.1032.62798.2
2.54-2.743.90.08357520.9940.0480.0963.03598.1
2.74-3.013.90.07557720.9940.0430.0863.4398.3
3.01-3.453.90.06557980.9950.0380.0753.8898.6
3.45-4.343.80.05458340.9960.0320.0633.8499.1
4.34-503.90.05357040.9960.0320.0625.85897.5

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7D28

7d28


Resolution: 1.6→33.08 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 48.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2477 2879 4.97 %
Rwork0.2314 55013 -
obs0.2323 57892 96.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.97 Å2 / Biso mean: 23.2151 Å2 / Biso min: 11.04 Å2
Refinement stepCycle: final / Resolution: 1.6→33.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3570 0 0 462 4032
Biso mean---32.11 -
Num. residues----474
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.620.3591320.41292302243485
1.62-1.650.38341550.37282586274196
1.65-1.680.37821390.35422541268095
1.68-1.720.32961250.35152595272095
1.72-1.750.32531240.32982605272996
1.75-1.790.39791160.32022633274996
1.79-1.830.33041400.29392594273496
1.83-1.880.32641220.29032622274496
1.88-1.930.32791260.28682625275196
1.93-1.980.28681230.26072649277297
1.98-2.050.27191290.26292613274297
2.05-2.120.27311260.24352651277797
2.12-2.210.30151390.23382652279197
2.21-2.310.26931400.23312653279397
2.31-2.430.28911480.2262657280598
2.43-2.580.25411430.22372657280098
2.58-2.780.26581550.21472651280698
2.78-3.060.21351340.20852691282598
3.06-3.50.181620.19392697285999
3.5-4.410.1821540.17212716287099
4.41-33.080.19031470.18992623277093

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