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- PDB-8a5c: Crystal structure of Deinococcus radiodurans Endonuclease III-1 Y... -

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Basic information

Entry
Database: PDB / ID: 8a5c
TitleCrystal structure of Deinococcus radiodurans Endonuclease III-1 Y100L 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 / 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: 1.951 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 14, 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)28,2474
Polymers27,8471
Non-polymers4003
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint-39 kcal/mol
Surface area11370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.526, 37.827, 36.550
Angle α, β, γ (deg.)90.000, 90.610, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Endonuclease III /


Mass: 27846.938 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-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 44.49 %
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: 1.95→44.629 Å / Num. obs: 17563 / % possible obs: 97.1 % / Redundancy: 3.2 % / Biso Wilson estimate: 48.37 Å2 / CC1/2: 0.997 / Net I/σ(I): 9.9
Reflection shellResolution: 1.95→2.05 Å / Num. unique obs: 2766 / CC1/2: 0.5

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Processing

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

Resolution: 1.951→44.629 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 31.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2473 1744 9.95 %
Rwork0.1937 15784 -
obs0.199 17528 96.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 199.34 Å2 / Biso mean: 75.5952 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 1.951→44.629 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1882 0 10 7 1899
Biso mean--55.53 51.03 -
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 (%)
1.951-2.00810.37381360.3566127195
2.0081-2.07290.35861440.3322129197
2.0729-2.1470.32491490.2889131197
2.147-2.23290.34771490.2767128796
2.2329-2.33450.35371410.2688131998
2.3345-2.45760.29251450.2485130997
2.4576-2.61160.30271410.2326132197
2.6116-2.81320.25331450.2326131597
2.8132-3.09620.28961480.2312133398
3.0962-3.54410.28141420.2158131097
3.5441-4.46450.20951520.1628134197
4.4645-44.6290.20361520.1461137697
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.02173.81324.28243.27293.83494.7489-0.09510.44083.0252-0.8650.00921.0933-1.6619-1.9590.06840.96430.187-0.04150.8140.16550.761713.516325.31522.38
27.60941.7835-0.35162.7418-3.41248.91170.2366-0.14810.19621.40950.95050.7877-0.2679-1.6977-0.95790.57850.14290.08960.92460.07960.69419.347812.285610.7923
34.2221-0.67754.56970.2077-0.37857.87230.1471-0.59480.4297-1.00810.552.6727-0.798-1.372-0.49470.87480.0849-0.3290.83430.08461.63526.0725-6.66869.3997
48.45980.46080.88645.0631-4.26243.8412-0.17491.619-0.1303-1.55290.27941.4327-1.24680.0408-0.0921.2531-0.1174-0.24020.9206-0.08191.099428.0042-12.83251.2111
54.7354.42444.47344.26953.35948.9127-0.0572-1.2873-0.32040.1371-0.2381-2.18710.79550.29350.28640.83950.0017-0.08080.6464-0.07341.091639.198-17.721911.0298
69.20315.25553.36734.91193.43227.0699-1.97171.47290.0255-3.28831.3214-1.3162-0.85140.69470.4821.273-0.28970.21050.7451-0.03530.871340.2973-11.54852.342
79.535-3.7319-1.8247.84664.91353.5453-0.1946-1.156-0.22782.11060.16940.12941.5793-0.26950.01841.0246-0.0208-0.21330.79760.00510.584936.4121-2.91122.2921
86.0805-3.26223.2123.4947-2.29134.36840.1491-0.18030.19070.0782-0.0401-0.25910.3548-0.0513-0.07460.48690.0244-0.05720.4217-0.01360.450226.8475.137810.3933
98.18013.7899-5.12358.3327-5.69034.8265-0.3563-0.67850.50160.00540.0907-0.50850.40120.91750.2580.3794-0.0056-0.01790.4908-0.10180.414122.637312.646210.2269
109.253-1.10135.44217.3852-2.27433.69350.6948-1.017-0.9531-0.2170.44470.57170.1412-1.5997-0.9750.5578-0.0215-0.0580.68570.13190.533114.20712.4237.6715
116.6814-1.0108-2.05827.4824-0.75698.64440.36060.4735-0.0604-0.1757-0.24330.24970.0562-0.8872-0.12380.4650.0237-0.11660.59420.05590.44357.925510.0556-3.2868
128.281-5.06673.59828.906-1.92948.3801-0.23961.4198-0.08840.1611-0.18340.31840.59891.08210.32840.71050.1447-0.0260.81390.11470.495514.47312.2881-10.0201
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 19:26)A19 - 26
2X-RAY DIFFRACTION2(chain A and resid 27:47)A27 - 47
3X-RAY DIFFRACTION3(chain A and resid 48:67)A48 - 67
4X-RAY DIFFRACTION4(chain A and resid 68:80)A68 - 80
5X-RAY DIFFRACTION5(chain A and resid 81:93)A81 - 93
6X-RAY DIFFRACTION6(chain A and resid 94:121)A94 - 121
7X-RAY DIFFRACTION7(chain A and resid 122:139)A122 - 139
8X-RAY DIFFRACTION8(chain A and resid 140:185)A140 - 185
9X-RAY DIFFRACTION9(chain A and resid 186:209)A186 - 209
10X-RAY DIFFRACTION10(chain A and resid 210:221)A210 - 221
11X-RAY DIFFRACTION11(chain A and resid 222:245)A222 - 245
12X-RAY DIFFRACTION12(chain A and resid 246:255)A246 - 255

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