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- PDB-7d2q: Crystal structure of MazE-MazF (Form-I) from Deinococcus radiodurans -

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Basic information

Entry
Database: PDB / ID: 7d2q
TitleCrystal structure of MazE-MazF (Form-I) 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: 1.99 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
C: Endoribonuclease MazF
D: AbrB/MazE/SpoVT family DNA-binding domain-containing protein
E: Endoribonuclease MazF
F: AbrB/MazE/SpoVT family DNA-binding domain-containing protein
G: Endoribonuclease MazF


Theoretical massNumber of molelcules
Total (without water)67,6976
Polymers67,6976
Non-polymers00
Water4,918273
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)45.486, 74.083, 136.852
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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.: 273 / 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: 27.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100 mM citric acid pH 3.5 and 25% PEG 3,350

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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: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 32418 / % possible obs: 99.9 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.034 / Rrim(I) all: 0.119 / Χ2: 0.938 / Net I/σ(I): 5.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.0313.20.77815880.8980.2210.8090.862100
2.03-2.0713.10.62816240.9380.180.6540.916100
2.07-2.1113.20.5415580.9460.1540.5610.918100
2.11-2.1513.20.48915970.9540.1390.5080.919100
2.15-2.213.20.43915950.9530.1250.4560.938100
2.2-2.2513.20.39415920.9710.1120.410.981100
2.25-2.3113.20.35316140.980.1010.3670.931100
2.31-2.3713.20.32315710.9770.0920.3360.976100
2.37-2.4413.10.28716120.9810.0820.2990.977100
2.44-2.5213.20.24316130.9810.0690.2530.95100
2.52-2.6113.20.22215930.9870.0630.230.967100
2.61-2.71130.18516140.990.0530.1930.981100
2.71-2.84130.14816170.9930.0430.1540.955100
2.84-2.9912.90.12616140.9940.0370.1310.947100
2.99-3.1712.80.10416280.9960.030.1080.915100
3.17-3.4212.60.08416190.9960.0250.0880.947100
3.42-3.7612.20.0716550.9970.0210.0740.943100
3.76-4.3111.90.05916560.9970.0180.0620.919100
4.31-5.4311.80.05316780.9980.0160.0550.844100
5.43-5010.30.06317800.9950.0210.0670.98299

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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: 1.99→37.3 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2229 1613 4.99 %
Rwork0.1782 30680 -
obs0.1805 32293 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.86 Å2 / Biso mean: 25.1675 Å2 / Biso min: 8.34 Å2
Refinement stepCycle: final / Resolution: 1.99→37.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3595 0 0 273 3868
Biso mean---33.29 -
Num. residues----475
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.99-2.040.27991080.2141213484
2.04-2.110.24541440.19882544100
2.11-2.190.25681140.19022577100
2.19-2.270.2411370.19282547100
2.27-2.380.22681160.19512570100
2.38-2.50.271280.19582574100
2.5-2.660.2751550.20212561100
2.66-2.860.25451390.19082572100
2.86-3.150.23521400.18892584100
3.15-3.610.19851500.16112594100
3.61-4.540.18661360.14072656100
4.55-100.19251460.18042767100

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