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- PDB-7d2m: Crystal structure of MazF (Form-II) from Deinococcus radiodurans -

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Basic information

Entry
Database: PDB / ID: 7d2m
TitleCrystal structure of MazF (Form-II) from Deinococcus radiodurans
ComponentsEndoribonuclease MazF
KeywordsTOXIN / MazEF toxin system / endonuclease
Function / homology
Function and homology information


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
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
TRIPHOSPHATE / Endoribonuclease MazF / PpGpp-regulated growth inhibitor ChpA/MazF, putative
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 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

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Assembly

Deposited unit
B: Endoribonuclease MazF
C: Endoribonuclease MazF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3815
Polymers24,9302
Non-polymers4503
Water6,053336
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-39 kcal/mol
Surface area9860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.451, 72.451, 112.517
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-459-

HOH

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Components

#1: Protein Endoribonuclease MazF


Mass: 12465.216 Da / Num. of mol.: 2
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: Chemical ChemComp-3PO / TRIPHOSPHATE


Mass: 257.955 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H5O10P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.96 Å3/Da / Density % sol: 58.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM Lithium Sulfate monohydrate, Tris HCl pH 8.5 and 30% PEG 4,000

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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: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.79→23 Å / Num. obs: 28465 / % possible obs: 99.4 % / Redundancy: 20 % / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.038 / Rrim(I) all: 0.186 / Χ2: 0.985 / Net I/σ(I): 8.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.8317.90.40713560.9420.0940.4180.81499.1
1.83-1.8618.10.39314250.9460.0910.4040.8299.7
1.86-1.918.10.37513850.9560.0860.3860.91699.6
1.9-1.9418.70.35513870.9490.080.3651.05699.7
1.94-1.9819.20.33314020.9660.0730.3411.07899.2
1.98-2.0319.50.31913910.9630.070.3271.16699.4
2.03-2.08200.30514180.9610.0660.3121.17199.6
2.08-2.1320.10.29814110.9710.0640.3051.20899.3
2.13-2.220.50.28213930.9750.060.2881.2399.8
2.2-2.2720.20.27814130.9790.0590.2841.26199.2
2.27-2.3520.10.25814030.9770.0550.2641.18999.1
2.35-2.4420.30.2513990.9810.0520.2561.18699.1
2.44-2.5520.40.23914200.9820.0490.2441.14999.7
2.55-2.6920.50.2314310.9850.0480.2351.1299.3
2.69-2.8620.90.21814130.9910.0440.2221.0598.7
2.86-3.0821.20.20314340.9880.0420.2071.00799.4
3.08-3.3822.40.18114490.9890.0370.1850.86299.9
3.38-3.87230.15914680.9920.0330.1630.75499.9
3.87-4.8722.30.1314900.9940.0280.1330.53999.3
4.87-2320.80.09715770.9920.0220.10.32998.3

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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: 1.79→22.91 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.46 / Phase error: 15.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1805 1422 5.06 %
Rwork0.1564 26691 -
obs0.1576 28113 97.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.37 Å2 / Biso mean: 21.5414 Å2 / Biso min: 8.35 Å2
Refinement stepCycle: final / Resolution: 1.79→22.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1666 0 23 336 2025
Biso mean--45.34 35.6 -
Num. residues----223
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.79-1.850.24191270.1848232486
1.85-1.930.18111490.1607260898
1.93-2.020.15841300.1523265898
2.02-2.120.17711420.1537267099
2.12-2.260.19071520.1479266199
2.26-2.430.18031150.1575269898
2.43-2.670.20131430.167271199
2.67-3.060.20051580.1621270699
3.06-3.850.15841560.14982778100
3.85-100.1731500.1534287797

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