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- PDB-7dhp: Crystal structure of MazF from Deinococcus radiodurans -

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Basic information

Entry
Database: PDB / ID: 7dhp
TitleCrystal structure of MazF from Deinococcus radiodurans
ComponentsEndoribonuclease MazF
KeywordsTOXIN / Toxin-antitoxin / ribonuclease
Function / homologymRNA interferase PemK-like / PemK-like, MazF-like toxin of type II toxin-antitoxin system / Plasmid maintenance toxin/Cell growth inhibitor / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / hydrolase activity / DNA binding / Endoribonuclease MazF
Function and homology information
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsZhao, Y. / Dai, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31670819 China
CitationJournal: Front Genet / Year: 2021
Title: MazEF Toxin-Antitoxin System-Mediated DNA Damage Stress Response in Deinococcus radiodurans.
Authors: Dai, J. / Chen, Z. / Hou, J. / Wang, Y. / Guo, M. / Cao, J. / Wang, L. / Xu, H. / Tian, B. / Zhao, Y.
History
DepositionNov 17, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 17, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5615
Polymers29,2732
Non-polymers2883
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-53 kcal/mol
Surface area9420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.490, 70.490, 111.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-404-

HOH

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Components

#1: Protein Endoribonuclease MazF


Mass: 14636.585 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: mazF / Plasmid: Pet28a / Production host: Escherichia coli (E. coli)
References: UniProt: A0A6G9BVQ8, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.36 Å3/Da / Density % sol: 47.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: ammonium sulfate, BIS-TRIS, PEG 3350

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→30 Å / Num. obs: 66360 / % possible obs: 96.1 % / Redundancy: 4.179 % / Biso Wilson estimate: 13.42 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.068 / Χ2: 0.958 / Net I/σ(I): 14.38
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.3-1.344.210.5163.5249530.8870.5999
1.34-1.374.2840.4144.2948950.9190.47299.6
1.37-1.414.290.3075.5447590.9490.3599.7
1.41-1.464.3010.2316.8446210.9720.26399.9
1.46-1.54.290.1798.1945180.9820.20599.9
1.5-1.564.3010.1449.9743620.9860.16599.7
1.56-1.624.3180.11711.6241810.9910.13499.8
1.62-1.684.2990.09314.0140620.9920.10699.6
1.68-1.764.2920.07816.2338950.9940.08999.6
1.76-1.844.2430.06618.1537110.9950.07699.9
1.84-1.944.2130.05620.5535650.9960.06499.6
1.94-2.064.1760.05122.7333720.9960.05999.6
2.06-2.24.1290.04824.3131740.9970.05599.4
2.2-2.384.0880.04525.2629450.9970.05299.3
2.38-2.614.0270.04325.8227360.9970.04999.1
2.61-2.913.8790.04126.0824440.9960.04897.4
2.91-3.363.730.03826.1719400.9960.04586.8
3.36-4.123.3520.04125.1512000.9940.04862.8
4.12-5.833.1120.04224.186890.9940.05145.3
5.83-302.8170.03721.983380.9960.04537.5

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KYS

6kys


Resolution: 1.3→27.83 Å / SU ML: 0.0884 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.5877 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1848 3277 4.94 %
Rwork0.1716 63076 -
obs0.1723 66353 96.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.64 Å2
Refinement stepCycle: LAST / Resolution: 1.3→27.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1648 0 15 200 1863
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01841781
X-RAY DIFFRACTIONf_angle_d1.65212436
X-RAY DIFFRACTIONf_chiral_restr0.1131263
X-RAY DIFFRACTIONf_plane_restr0.0099321
X-RAY DIFFRACTIONf_dihedral_angle_d23.0908641
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.320.2231310.21582759X-RAY DIFFRACTION98.6
1.32-1.340.22961300.1982808X-RAY DIFFRACTION99.39
1.34-1.370.1941410.1942804X-RAY DIFFRACTION99.76
1.37-1.390.19311520.19312813X-RAY DIFFRACTION99.76
1.39-1.410.1781500.1782785X-RAY DIFFRACTION99.59
1.41-1.440.20011540.1792808X-RAY DIFFRACTION99.87
1.44-1.470.19081360.182823X-RAY DIFFRACTION99.8
1.47-1.50.1841210.16612833X-RAY DIFFRACTION99.9
1.5-1.540.17681690.16292797X-RAY DIFFRACTION99.63
1.54-1.580.17861570.1662816X-RAY DIFFRACTION99.97
1.58-1.620.16691450.1612805X-RAY DIFFRACTION99.66
1.62-1.670.16331530.15752821X-RAY DIFFRACTION99.6
1.67-1.720.17091450.16122840X-RAY DIFFRACTION99.53
1.72-1.780.15641490.15322822X-RAY DIFFRACTION99.76
1.78-1.850.17491470.16542855X-RAY DIFFRACTION99.9
1.85-1.940.15311530.15052810X-RAY DIFFRACTION99.63
1.94-2.040.15471510.152846X-RAY DIFFRACTION99.67
2.04-2.170.16821390.14772879X-RAY DIFFRACTION99.51
2.17-2.330.15951280.15572862X-RAY DIFFRACTION99.3
2.33-2.570.17931640.16482855X-RAY DIFFRACTION99.11
2.57-2.940.17741520.16752845X-RAY DIFFRACTION97.5
2.94-3.70.18811280.18292397X-RAY DIFFRACTION81.24
3.7-27.830.3509820.27521393X-RAY DIFFRACTION45.11
Refinement TLS params.Method: refined / Origin x: -25.1792162903 Å / Origin y: -1.70515737433 Å / Origin z: -6.02644325283 Å
111213212223313233
T0.108242265231 Å20.00212392574277 Å20.00166640195705 Å2-0.103275415429 Å20.00658910891503 Å2--0.113168660694 Å2
L0.387807477435 °20.219892418539 °20.00177743028413 °2-0.788540508466 °2-0.140982189018 °2--0.720473507441 °2
S0.0138445017582 Å °0.0148031128693 Å °0.0173607047783 Å °0.0383667322615 Å °-0.0232778415847 Å °0.0301352643075 Å °-0.0153372052331 Å °0.0288310271924 Å °0.000109929168231 Å °
Refinement TLS groupSelection details: all

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