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- PDB-8a5f: Crystal structure of Deinococcus radiodurans Endonuclease III-1 R... -

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Basic information

Entry
Database: PDB / ID: 8a5f
TitleCrystal structure of Deinococcus radiodurans Endonuclease III-1 R61Q variant
ComponentsEndonuclease III
KeywordsLYASE / DNA glycosylase / resistant bacterium / Deinococcus radiodurans / mutations
Function / homology
Function and homology information


oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity / base-excision repair, AP site formation / DNA-(apurinic or apyrimidinic site) endonuclease activity / nucleotide-excision repair / 4 iron, 4 sulfur cluster binding / endonuclease activity / metal ion binding
Similarity search - Function
Endonuclease III, iron-sulphur binding site / Endonuclease III iron-sulfur binding region signature. / Endonuclease III-like, iron-sulphur cluster loop motif / FES / HhH-GPD superfamily base excision DNA repair protein / Helix-hairpin-helix, base-excision DNA repair, C-terminal / HhH-GPD domain / endonuclease III / DNA glycosylase
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / Endonuclease III
Similarity search - Component
Biological speciesDeinococcus radiodurans R1 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsBorges, P.T. / Rollo, F. / Moe, E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Foundation for Science and Technology (FCT) United Kingdom
CitationJournal: Molecules / Year: 2022
Title: Disentangling Unusual Catalytic Properties and the Role of the [4Fe-4S] Cluster of Three Endonuclease III from the Extremophile D. radiodurans.
Authors: Rollo, F. / Borges, P.T. / Silveira, C.M. / Rosa, M.T.G. / Todorovic, S. / Moe, E.
History
DepositionJun 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endonuclease III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2684
Polymers27,8681
Non-polymers4003
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area570 Å2
ΔGint-40 kcal/mol
Surface area11400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.318, 38.040, 36.353
Angle α, β, γ (deg.)90.000, 90.960, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-503-

HOH

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Components

#1: Protein Endonuclease III


Mass: 27867.889 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans R1 (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Gene: DR_2438 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9RRQ0
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.22 Å3/Da / Density % sol: 44.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M bicine pH 9.0, 30% (w/v) PEG 500 MME and 0.1 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.38→44.823 Å / Num. obs: 50163 / % possible obs: 98.9 % / Redundancy: 2.9 % / Biso Wilson estimate: 23.89 Å2 / CC1/2: 0.99 / Net I/σ(I): 8.9
Reflection shellResolution: 1.38→1.47 Å / Num. unique obs: 8090 / CC1/2: 0.46

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXdev_3026refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Endo III-1 wild-type

Resolution: 1.38→44.823 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 21.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1804 2013 4.01 %
Rwork0.1509 48140 -
obs0.1521 50153 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.98 Å2 / Biso mean: 36.6245 Å2 / Biso min: 16.17 Å2
Refinement stepCycle: final / Resolution: 1.38→44.823 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1884 0 10 165 2059
Biso mean--26.19 42.65 -
Num. residues----237
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3802-1.41470.34611400.3069339498
1.4147-1.45290.28991480.25973459100
1.4529-1.49570.2621380.2086338899
1.4957-1.5440.2251430.1805341999
1.544-1.59910.20121440.151337198
1.5991-1.66320.20811440.14673464100
1.6632-1.73890.221430.14823454100
1.7389-1.83050.20921450.13653451100
1.8305-1.94520.18711390.1347343899
1.9452-2.09540.181440.1346342898
2.0954-2.30630.15471440.1309343999
2.3063-2.640.19111450.1438345499
2.64-3.32590.16761440.172345098
3.3259-44.8230.16811520.144353198

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