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- PDB-7d2p: Crystal structure of MazE-MazF (Form-II) from Deinococcus radiodurans -

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Basic information

Entry
Database: PDB / ID: 7d2p
TitleCrystal structure of MazE-MazF (Form-II) 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: 2.07 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
B: Endoribonuclease MazF
C: Endoribonuclease MazF
D: Endoribonuclease MazF
E: AbrB/MazE/SpoVT family DNA-binding domain-containing protein
F: AbrB/MazE/SpoVT family DNA-binding domain-containing protein


Theoretical massNumber of molelcules
Total (without water)67,6976
Polymers67,6976
Non-polymers00
Water4,270237
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, CRYSTAL STRUCTURE SHOWS HETERO-TRIMER DUE TO AUTOCLEAVAGE
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.824, 42.327, 64.998
Angle α, β, γ (deg.)96.510, 97.820, 86.710
Int Tables number1
Space group name H-MP1

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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.: 237 / 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: 1.59 Å3/Da / Density % sol: 22.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M succinic acid pH 7.0 and 12% w/v 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: 0.97935 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 28134 / % possible obs: 97.2 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.038 / Rrim(I) all: 0.074 / Χ2: 0.791 / Net I/σ(I): 8.4 / Num. measured all: 104692
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.033.90.36514110.9020.2150.4240.83296.2
2.03-2.073.80.33813590.9190.20.3930.84996.9
2.07-2.113.80.25814320.9720.1560.3021.14696.4
2.11-2.153.90.2414070.9380.1410.2790.88797.9
2.15-2.23.90.20613880.9540.1220.2390.85896.7
2.2-2.253.80.20814420.9540.1240.2420.92497.5
2.25-2.313.60.18113630.9480.1120.2131.21196.5
2.31-2.373.90.1514400.9690.0880.1740.82297.3
2.37-2.443.80.12713750.9780.0750.1480.81997.9
2.44-2.523.80.11714370.9790.0690.1360.80997.8
2.52-2.613.80.10314060.9810.0620.120.81497.6
2.61-2.713.80.09114200.9820.0540.1060.81498.3
2.71-2.843.80.07114510.9870.0430.0830.74598.1
2.84-2.993.70.05913990.9880.0360.0690.6898
2.99-3.173.70.0514180.9910.030.0590.65597.9
3.17-3.423.60.0414220.9920.0240.0470.54598.8
3.42-3.763.50.03414060.9930.0210.0410.54197.8
3.76-4.313.50.03214280.9930.020.0370.52797.8
4.31-5.433.50.03114010.9930.020.0370.56997.1
5.43-503.30.03413290.9920.0220.0410.66191.9

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7D28

7d28


Resolution: 2.07→29.4 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.918 / SU B: 5.087 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.291 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1962 8.3 %RANDOM
Rwork0.1678 ---
obs0.173 21791 93.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.74 Å2 / Biso mean: 25.914 Å2 / Biso min: 11.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20.01 Å20.02 Å2
2---0.01 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 2.07→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3665 0 0 237 3902
Biso mean---37.23 -
Num. residues----489
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133749
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173499
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.6345105
X-RAY DIFFRACTIONr_angle_other_deg1.3021.5758061
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6275481
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.47820.316190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.41415556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1791534
X-RAY DIFFRACTIONr_chiral_restr0.0670.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024269
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02809
LS refinement shellResolution: 2.074→2.127 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 124 -
Rwork0.193 1304 -
all-1428 -
obs--76.65 %

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