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- PDB-7d28: Crystal structure of MazF (Form-I) from Deinococcus radiodurans -

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Basic information

Entry
Database: PDB / ID: 7d28
TitleCrystal structure of MazF (Form-I) 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
Endoribonuclease MazF / PpGpp-regulated growth inhibitor ChpA/MazF, putative
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 16, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,82610
Polymers49,8614
Non-polymers9656
Water8,899494
1
A: Endoribonuclease MazF
D: Endoribonuclease MazF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4135
Polymers24,9302
Non-polymers4833
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-5 kcal/mol
Surface area9900 Å2
MethodPISA
2
B: Endoribonuclease MazF
C: Endoribonuclease MazF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4135
Polymers24,9302
Non-polymers4833
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-13 kcal/mol
Surface area10190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.542, 74.976, 120.103
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 (bacteria)
References: UniProt: A0A6G9BVQ8, UniProt: Q9RX98*PLUS, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 494 / 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: 2.19 Å3/Da / Density % sol: 43.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 5000 MME, 100 mM MES pH 6.5 and 200 mM Ammonium sulfate

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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: Jul 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 71103 / % possible obs: 100 % / Redundancy: 14.4 % / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.021 / Rrim(I) all: 0.081 / Χ2: 0.997 / Net I/σ(I): 7.2 / Num. measured all: 1021009
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.5314.40.90835200.9220.2460.9410.9100
1.53-1.5514.50.78834860.9280.2130.8170.93100
1.55-1.5814.50.72235010.940.1950.7480.947100
1.58-1.6214.50.61535240.960.1660.6370.966100
1.62-1.6514.50.51434980.9660.1390.5331.011100
1.65-1.6914.50.4235240.9790.1130.4351.014100
1.69-1.7314.50.35335170.9830.0950.3661.032100
1.73-1.7814.50.28435260.9880.0770.2941.052100
1.78-1.8314.50.24535180.9920.0660.2541.071100
1.83-1.8914.50.20535140.9940.0550.2131.1100
1.89-1.9614.50.16235360.9960.0440.1681.067100
1.96-2.0414.50.12935480.9970.0350.1341.064100
2.04-2.1314.50.10835520.9970.0290.1121.056100
2.13-2.2414.50.09435350.9980.0250.0971.054100
2.24-2.3814.50.08235590.9980.0220.0851.009100
2.38-2.5614.50.06935870.9980.0190.0710.97100
2.56-2.8214.40.05835790.9990.0160.0610.934100
2.82-3.2314.30.0536200.9990.0140.0510.933100
3.23-4.07140.04236530.9990.0120.0440.928100
4.07-5012.60.04138060.9990.0120.0430.90399.2

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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: 5ck9

5ck9


Resolution: 1.5→28.82 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.208 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2 3502 4.9 %RANDOM
Rwork0.1709 ---
obs0.1723 67509 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 117.98 Å2 / Biso mean: 17.64 Å2 / Biso min: 5.57 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.5→28.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3308 0 60 494 3862
Biso mean--64.56 33.4 -
Num. residues----442
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0133446
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173228
X-RAY DIFFRACTIONr_angle_refined_deg1.8741.6354690
X-RAY DIFFRACTIONr_angle_other_deg1.5171.5727456
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5535438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.09620172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.31615502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8441532
X-RAY DIFFRACTIONr_chiral_restr0.1020.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023874
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02734
LS refinement shellResolution: 1.5→1.538 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.25 249 -
Rwork0.243 4876 -
obs--99.11 %

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