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- PDB-8a5g: Crystal structure of Deinococcus radiodurans Endonuclease III-3 d... -

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Basic information

Entry
Database: PDB / ID: 8a5g
TitleCrystal structure of Deinococcus radiodurans Endonuclease III-3 double mutant
ComponentsEndonuclease III
KeywordsLYASE / DNA glycosylase / resistant bacterium / Deinococcus radiodurans / Endonuclease / mutations
Function / homology
Function and homology information


catalytic activity, acting on DNA / base-excision repair / 4 iron, 4 sulfur cluster binding / endonuclease activity / metal ion binding
Similarity search - Function
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, putative
Similarity search - Component
Biological speciesDeinococcus radiodurans R1 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 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)30,0884
Polymers29,6661
Non-polymers4233
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint-43 kcal/mol
Surface area11720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.345, 38.827, 71.988
Angle α, β, γ (deg.)90.000, 99.710, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Endonuclease III


Mass: 29665.721 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_0928 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9RVU4
#2: 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
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 1.97 Å3/Da / Density % sol: 37.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.2 M ammonium formate and 2.2 M ammonium sulfate

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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: 1.89→44.5 Å / Num. obs: 19937 / % possible obs: 99.1 % / Redundancy: 3.3 % / Biso Wilson estimate: 30.99 Å2 / CC1/2: 0.99 / Net I/σ(I): 13.7
Reflection shellResolution: 1.89→1.99 Å / Num. unique obs: 3111 / CC1/2: 0.5

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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-3 wild-type

Resolution: 1.89→44.5 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.45 / Phase error: 34.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2885 1992 10 %
Rwork0.2384 17930 -
obs0.2435 19922 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.08 Å2 / Biso mean: 50.4252 Å2 / Biso min: 19.33 Å2
Refinement stepCycle: final / Resolution: 1.89→44.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1900 0 10 73 1983
Biso mean--44.78 44.24 -
Num. residues----238
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.89-1.93390.38251330.3608120995
1.9339-1.98620.36581420.34661276100
1.9862-2.04470.37821440.3314129499
2.0447-2.11070.42151390.33211247100
2.1107-2.18610.33931420.30431276100
2.1861-2.27360.31191420.2948127499
2.2736-2.37710.31591430.2881128499
2.3771-2.50240.3431400.2757126599
2.5024-2.65920.3191430.27141291100
2.6592-2.86450.32281430.266127499
2.8645-3.15270.31411430.25551291100
3.1527-3.60870.28091430.2186130299
3.6087-4.54590.23211460.1736130299
4.5459-44.50.23971490.1964134599
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)
12.8680.8555-1.79170.3325-0.68321.40580.1244-0.539-0.03790.4554-0.2889-0.1927-0.84160.48460.22231.6705-0.04060.02650.50170.07360.383623.06734.071141.7042
20.76670.4362-0.37360.6112-0.5390.4712-0.1748-0.0126-0.10130.39530.16550.084-0.178-0.172-0.00351.35480.17320.41690.38720.13030.50956.774231.170728.0753
31.49932.39350.48885.5356-1.10482.34240.19390.3163-0.03930.8694-0.05650.0672-0.0177-0.2108-0.16990.24710.01270.01450.4248-0.02910.206723.796529.01839.1165
43.0322.85013.81514.68175.0555.8780.1273-0.49630.31330.4257-0.86510.77360.2054-0.96820.71270.8560.31310.11240.8044-0.03060.388618.690441.95767.9324
54.72052.3788-0.79416.12572.44044.722-0.02330.3162-0.1612-0.29050.02690.5352-0.2981-0.4697-0.00030.12910.0207-0.04590.48520.06130.261724.617835.3206-1.5168
69.0784-1.6335-4.39470.9444-0.50384.9396-0.04840.415-0.6198-0.0976-0.2114-0.27510.13210.51630.22990.11460.00340.05990.5188-0.07810.714437.633930.5389-0.2097
78.7076-4.15561.67275.38510.0138.30530.20230.08010.31650.045-0.0729-0.8976-0.54150.291-0.13520.1672-0.047-0.00620.42110.04360.351932.774142.513-1.6265
85.5434-0.19844.68929.7317-0.76174.00230.0549-0.1491-0.31390.49490.0566-0.2131-0.202-0.2313-0.11980.49970.175-0.12110.7157-0.0380.290630.473546.56285.1575
91.9521-0.72130.40940.6144-0.03260.82360.2248-0.1632-0.61250.2449-0.1092-0.4560.28450.2934-0.13330.2509-0.0459-0.43760.48770.09510.814139.867534.19639.0502
106.33880.5086-1.36818.4408-4.17322.3890.03580.8723-0.5483-0.33970.21240.27710.4182-0.1713-0.31310.25830.0179-0.33270.48340.02690.594535.483723.73178.803
113.94640.3611.69820.2691-0.99346.33410.0378-0.5382-0.19650.4835-0.1365-0.33590.501-0.02730.08640.95650.07-0.28460.4310.0160.4131.955121.186422.457
120.7547-0.1195-0.58851.23970.90481.04880.08680.18390.07090.7718-0.0128-0.1492-0.5414-0.0324-0.02580.96510.0306-0.00950.35230.03030.190122.382333.832820.8571
130.15740.15170.15890.93411.08661.2680.0669-0.03890.05730.15220.1535-0.0951-0.09250.201-0.17581.45620.10330.16930.269-0.10570.249819.234941.460532.4734
140.19570.2450.00340.305-0.01950.62520.18740.26230.21990.40540.05150.1345-0.4836-0.12560.0591.30720.1260.22720.44870.08550.139612.681934.541723.1199
150.04760.0420.14660.47990.230.4710.0469-0.08480.1495-0.129-0.01910.0419-0.3589-0.156-0.04171.51180.33810.60190.65040.05340.60780.394143.350228.3707
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 87:92)A87 - 92
2X-RAY DIFFRACTION2(chain A and resid 93:114)A93 - 114
3X-RAY DIFFRACTION3(chain A and resid 115:135)A115 - 135
4X-RAY DIFFRACTION4(chain A and resid 136:139)A136 - 139
5X-RAY DIFFRACTION5(chain A and resid 140:154)A140 - 154
6X-RAY DIFFRACTION6(chain A and resid 155:161)A155 - 161
7X-RAY DIFFRACTION7(chain A and resid 162:175)A162 - 175
8X-RAY DIFFRACTION8(chain A and resid 176:181)A176 - 181
9X-RAY DIFFRACTION9(chain A and resid 182:199)A182 - 199
10X-RAY DIFFRACTION10(chain A and resid 200:203)A200 - 203
11X-RAY DIFFRACTION11(chain A and resid 204:220)A204 - 220
12X-RAY DIFFRACTION12(chain A and resid 221:259)A221 - 259
13X-RAY DIFFRACTION13(chain A and resid 260:270)A260 - 270
14X-RAY DIFFRACTION14(chain A and resid 271:308)A271 - 308
15X-RAY DIFFRACTION15(chain A and resid 309:324)A309 - 324

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