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- PDB-8dwf: Glycosylase MutY variant E43S in complex with DNA containing d(8-... -

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Basic information

Entry
Database: PDB / ID: 8dwf
TitleGlycosylase MutY variant E43S in complex with DNA containing d(8-oxo-G) paired with substrate adenine
Components
  • Adenine DNA glycosylase
  • DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3')
  • DNA (5'-D(*TP*GP*TP*CP*CP*AP*AP*GP*TP*CP*T)-3')
KeywordsHYDROLASE/DNA / Protein-DNA complex / DNA repair / Base Excision Repair / HYDROLASE / HYDROLASE-DNA complex
Function / homology
Function and homology information


adenine/guanine mispair binding / adenine glycosylase / DNA N-glycosylase activity / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / purine-specific mismatch base pair DNA N-glycosylase activity / oxidized purine DNA binding / mismatch repair / base-excision repair / 4 iron, 4 sulfur cluster binding / DNA binding / metal ion binding
Similarity search - Function
A/G-specific adenine glycosylase MutY / Iron-sulfur binding domain of endonuclease III / Adenine/Thymine-DNA glycosylase / MutY, C-terminal / NUDIX domain / Helix-hairpin-helix motif / Endonuclease III-like, iron-sulphur cluster loop motif / FES / Helix-hairpin-helix motif / HhH-GPD superfamily base excision DNA repair protein ...A/G-specific adenine glycosylase MutY / Iron-sulfur binding domain of endonuclease III / Adenine/Thymine-DNA glycosylase / MutY, C-terminal / NUDIX domain / Helix-hairpin-helix motif / Endonuclease III-like, iron-sulphur cluster loop motif / FES / Helix-hairpin-helix motif / HhH-GPD superfamily base excision DNA repair protein / Helix-hairpin-helix, base-excision DNA repair, C-terminal / HhH-GPD domain / endonuclease III / DNA glycosylase / NUDIX hydrolase-like domain superfamily
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / DNA / DNA (> 10) / Adenine DNA glycosylase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsRusselburg, L.P. / Demir, M. / David, S.S. / Horvath, M.P.
Funding support United States, 4items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1905304 United States
National Science Foundation (NSF, United States)1905249 United States
National Science Foundation (NSF, United States)1610721 United States
National Science Foundation (NSF, United States)1608934 United States
CitationJournal: To Be Published
Title: Structural Basis for Base Engagement and Stereochemistry Revealed by Alteration of Catalytic Residue Glu43 in DNA Repair Glycosylase MutY
Authors: Russelburg, L.P. / Demir, M. / Cedeno, K. / David, S.S. / Horvath, M.P.
History
DepositionAug 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenine DNA glycosylase
B: DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3')
C: DNA (5'-D(*TP*GP*TP*CP*CP*AP*AP*GP*TP*CP*T)-3')
D: Adenine DNA glycosylase
E: DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3')
F: DNA (5'-D(*TP*GP*TP*CP*CP*AP*AP*GP*TP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,19016
Polymers96,9586
Non-polymers1,23210
Water1,67593
1
A: Adenine DNA glycosylase
B: DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3')
C: DNA (5'-D(*TP*GP*TP*CP*CP*AP*AP*GP*TP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0958
Polymers48,4793
Non-polymers6165
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-52 kcal/mol
Surface area18030 Å2
MethodPISA
2
D: Adenine DNA glycosylase
E: DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3')
F: DNA (5'-D(*TP*GP*TP*CP*CP*AP*AP*GP*TP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0958
Polymers48,4793
Non-polymers6165
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-53 kcal/mol
Surface area17740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.080, 137.900, 74.520
Angle α, β, γ (deg.)90.000, 101.440, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AD

#1: Protein Adenine DNA glycosylase / oxoG:A-specific adenine glycosylase


Mass: 41731.559 Da / Num. of mol.: 2 / Mutation: E43S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: mutY / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P83847, adenine glycosylase

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DNA chain , 2 types, 4 molecules BECF

#2: DNA chain DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3')


Mass: 3423.249 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*GP*TP*CP*CP*AP*AP*GP*TP*CP*T)-3')


Mass: 3324.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 103 molecules

#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.57 Å3/Da / Density % sol: 52.2 % / Description: Yellow, rod, rectangular
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: PEG 4000, calcium acetate, ethylene glycol, Tris.HCl, beta-mercaptoethanol
Temp details: Ambient

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 11, 2020
RadiationMonochromator: Water-cooled flat double Si(111) Khozu monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 2.6→73 Å / Num. obs: 58172 / % possible obs: 98.7 % / Redundancy: 2.58 % / Biso Wilson estimate: 55.18 Å2 / CC1/2: 0.981 / Rmerge(I) obs: 0.191 / Net I/σ(I): 5.62
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 2.57 % / Rmerge(I) obs: 2.07 / Mean I/σ(I) obs: 0.79 / Num. unique obs: 4259 / CC1/2: 0.091 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6U7T

6u7t


Resolution: 2.6→73 Å / SU ML: 0.4774 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.1517
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2533 1506 2.6 %
Rwork0.2068 56432 -
obs0.2081 57938 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.15 Å2
Refinement stepCycle: LAST / Resolution: 2.6→73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5411 864 44 93 6412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01516562
X-RAY DIFFRACTIONf_angle_d1.26039133
X-RAY DIFFRACTIONf_chiral_restr0.06591023
X-RAY DIFFRACTIONf_plane_restr0.01071019
X-RAY DIFFRACTIONf_dihedral_angle_d18.03552405
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.680.36571290.34464978X-RAY DIFFRACTION95.49
2.68-2.780.36211300.32785084X-RAY DIFFRACTION97.71
2.78-2.890.36721620.31545106X-RAY DIFFRACTION98.28
2.89-3.020.40761340.28515156X-RAY DIFFRACTION99.03
3.02-3.180.28661350.25545151X-RAY DIFFRACTION98.8
3.18-3.380.29721290.23225162X-RAY DIFFRACTION98.66
3.38-3.640.26731320.20065155X-RAY DIFFRACTION98.77
3.64-4.010.27331460.18445154X-RAY DIFFRACTION98.84
4.01-4.590.1981410.15245203X-RAY DIFFRACTION99.57
4.59-5.780.20831420.16765137X-RAY DIFFRACTION98.84
5.78-730.19111260.18365146X-RAY DIFFRACTION98.32
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)
10.78906753712-0.3403687859170.1467365215130.839646194221-0.3307876688711.161546398430.01809970153840.002827796396120.0602958550842-0.01236757837970.0162150826620.01101149523670.0909526296204-0.131873077252.04450736874E-50.336432125637-0.01322164915120.02533639775910.3950760474950.02742321648020.443142892932.497735253866.69053649546.2705318003
20.5727668572090.126304078724-0.1204371706040.2440980493690.05895221223980.2244224177850.02509298355-0.1927316562190.1055081727630.2500246662690.0907310263426-0.07215704437090.2076501021250.1231351501132.61770872325E-50.6213532231340.0877093571529-0.09597592583380.5265494844110.0109851772950.50250789790624.0692238794-1.5811750946134.5144946014
30.845100568119-0.12272041151-0.1610863812160.5219784023450.2471302220071.27313481360.08445566664940.0192742241312-0.0715143074810.0356807986246-0.0337824498299-0.0708427798545-0.1244418219160.02687340610751.15260729717E-50.345127205944-0.00101655517339-0.01595311532430.387334482945-0.02595354410940.39503879129522.017130882-41.85282307046.76662925357
40.4839998444260.0468602342965-0.2682194513090.5737388621910.01506388914260.3105997083530.0446540755352-0.1231858574210.04656833768630.2461208514730.01161830091430.117015222791-0.0413780382035-0.2218082142085.37813995507E-50.623914733154-0.001615544119060.1460472849680.569233305379-0.04109311724430.405586372398-0.297059587493-33.186746552833.5689095365
50.2917960121840.0620624741415-0.205675270722-0.009322166396250.171847275360.1612846355550.2641934658470.0715268948074-0.0156847620417-0.100577286237-0.338715586953-0.01251112476950.2534875563160.0974100061840.0003099145865080.4933524068630.0242380795193-0.03700824402910.4600708410950.02576464756970.47430265767515.8136780779-0.02235892235811.7533166566
60.339964821013-0.0909201427793-0.01440254608810.01899622260270.02743652221720.218592941530.3207041294990.0710614449070.193420241270.131781111129-0.4447217429180.194196356438-0.247448118712-0.1743510267260.0002539473488860.530334885730.0494352254228-0.008066351263890.503121573458-0.04202712948020.5452504573388.69635370853-34.947706124211.576768884
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and (resid 6:228 or resid 401 or resid 403))AA - C6 - 4031
22(chain A and (resid 229:359 or resid 404))AA - D229 - 404224
33(chain D and (resid 4:228 or resid 401 or resid 403))DI - K4 - 4031
44(chain D and (resid 229:360 or resid 404))DI - L229 - 404226
55((chain B and resid 1:11) or (chain C and resid 12:22))B - CF - H1 - 22
66((chain E and resid 1:11) or (chain F and resid 12:22))E - FN - P1 - 22

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