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- PDB-3gq3: MutM encountering an intrahelical 8-oxoguanine (oxoG) lesion in E... -

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Basic information

Entry
Database: PDB / ID: 3gq3
TitleMutM encountering an intrahelical 8-oxoguanine (oxoG) lesion in EC5-loop deletion complex
Components
  • DNA (5'-D(*AP*GP*GP*TP*AP*GP*AP*CP*CP*CP*GP*GP*AP*CP*GP*C)-3')
  • DNA (5'-D(*TP*GP*CP*GP*TP*CP*CP*GP*(8OG)P*GP*TP*CP*TP*AP*CP*C)-3')
  • DNA glycosylase
KeywordsLyase/DNA / DNA glycosylase / DNA repair / damage search / base extrusion / disulfide crosslinking / DNA damage / DNA-binding / Glycosidase / Hydrolase / Lyase / Metal-binding / Multifunctional enzyme / Zinc-finger / Lyase-DNA COMPLEX
Function / homology
Function and homology information


DNA-formamidopyrimidine glycosylase / oxidized purine nucleobase lesion DNA N-glycosylase activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair / damaged DNA binding / zinc ion binding
Similarity search - Function
Formamidopyrimidine-DNA glycosylase / Zinc finger, DNA glycosylase/AP lyase-type / Zinc finger, FPG/IleRS-type / DNA glycosylase/AP lyase, zinc finger domain, DNA-binding site / Zinc finger found in FPG and IleRS / Zinc finger FPG-type signature. / Zinc finger FPG-type profile. / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase H2TH domain / N-terminal domain of MutM-like DNA repair proteins ...Formamidopyrimidine-DNA glycosylase / Zinc finger, DNA glycosylase/AP lyase-type / Zinc finger, FPG/IleRS-type / DNA glycosylase/AP lyase, zinc finger domain, DNA-binding site / Zinc finger found in FPG and IleRS / Zinc finger FPG-type signature. / Zinc finger FPG-type profile. / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase H2TH domain / N-terminal domain of MutM-like DNA repair proteins / Formamidopyrimidine-DNA glycosylase N-terminal domain / Formamidopyrimidine-DNA glycosylase N-terminal domain / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase, catalytic domain / Formamidopyrimidine-DNA glycosylase catalytic domain profile. / Formamidopyrimidine-DNA glycosylase H2TH domain / DNA glycosylase/AP lyase, H2TH DNA-binding / Helicase, Ruva Protein; domain 3 - #50 / Helicase, Ruva Protein; domain 3 / Ribosomal protein S13-like, H2TH / Alpha-Beta Barrel / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Formamidopyrimidine-DNA glycosylase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.83 Å
AuthorsBanerjee, A. / Qi, Y. / Verdine, G.L.
CitationJournal: Nature / Year: 2009
Title: Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme.
Authors: Qi, Y. / Spong, M.C. / Nam, K. / Banerjee, A. / Jiralerspong, S. / Karplus, M. / Verdine, G.L.
History
DepositionMar 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 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: DNA glycosylase
B: DNA (5'-D(*AP*GP*GP*TP*AP*GP*AP*CP*CP*CP*GP*GP*AP*CP*GP*C)-3')
C: DNA (5'-D(*TP*GP*CP*GP*TP*CP*CP*GP*(8OG)P*GP*TP*CP*TP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7504
Polymers38,6853
Non-polymers651
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-19 kcal/mol
Surface area14470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.085, 92.411, 105.836
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA glycosylase /


Mass: 28869.523 Da / Num. of mol.: 1 / Mutation: Q166C, 220-235 deletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: MutM / Plasmid: pET24B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) PlysS
References: UniProt: P84131, DNA-(apurinic or apyrimidinic site) lyase
#2: DNA chain DNA (5'-D(*AP*GP*GP*TP*AP*GP*AP*CP*CP*CP*GP*GP*AP*CP*GP*C)-3')


Mass: 4933.206 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*TP*GP*CP*GP*TP*CP*CP*GP*(8OG)P*GP*TP*CP*TP*AP*CP*C)-3')


Mass: 4882.140 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O

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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: 2.85 Å3/Da / Density % sol: 56.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 8K, sodium cacodylate, glycerol, pH 7.0, vapor diffusion, hanging drop, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 8K11
2sodium cacodylate11
3glycerol11
4PEG 8K12
5sodium cacodylate12
6glycerol12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1
DetectorType: ADSC / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 38683 / % possible obs: 96.7 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.061 / Χ2: 1.026 / Net I/σ(I): 21.938
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.83-1.93.90.3430441.031177.3
1.9-1.974.30.26736771.055193.3
1.97-2.064.70.20538871.048199
2.06-2.174.80.1639191.037199.4
2.17-2.314.90.12739381.031199.5
2.31-2.484.80.10439570.998199.7
2.48-2.734.80.08539741.038199.7
2.73-3.134.80.06640020.994199.7
3.13-3.944.60.04440471.012199.8
3.94-504.60.03542381.027199.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.4.0066refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
CNSphasing
RefinementResolution: 1.83→45.93 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.071 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.209 1861 5 %RANDOM
Rwork0.182 ---
obs0.183 37193 96.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 115.51 Å2 / Biso mean: 33.499 Å2 / Biso min: 9.81 Å2
Refinement stepCycle: LAST / Resolution: 1.83→45.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1959 552 1 266 2778
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222641
X-RAY DIFFRACTIONr_angle_refined_deg1.4942.2443690
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7175252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.90921.22290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.21915345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2461527
LS refinement shellResolution: 1.83→1.874 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 86 -
Rwork0.211 1806 -
all-1892 -
obs--88 %
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)
10.8052-0.04070.04980.7610.26160.9499-0.046-0.12810.0227-0.03590.0045-0.03270.00930.00090.04150.00490.0013-0.00910.0123-0.0144-0.111218.735-15.5679.128
21.1797-0.7854-0.57351.18460.49570.44050.04750.00890.1365-0.0429-0.0606-0.1281-0.0418-0.08020.0130.05130.0086-0.0208-0.0034-0.0213-0.097115.611-10.9054.231
32.851-2.0318-1.56791.46671.23631.6141-0.0075-0.28910.11980.03250.0725-0.1636-0.03720.103-0.06510.0223-0.00180.00380.0892-0.0447-0.146925.738-14.90615.121
40.453-0.2747-0.27470.32130.15810.2609-0.0342-0.10350.0411-0.00970.0373-0.0247-0.0010.0292-0.00310.04020.01630.00870.0516-0.0091-0.128520.178-17.8511.729
512.3239-0.26056.723915.171711.428112.49540.2726-0.33760.5044-0.3692-0.77650.5140.1451-0.80390.5039-0.04220.045-0.04060.0252-0.1212-0.08813.318-7.8678.159
60.0606-0.4216-0.35382.93462.46272.0666-0.00320.0513-0.2717-0.401-0.7510.4187-0.2342-0.36640.75410.00280.1335-0.14640.0372-0.2167-0.07412.46.66119.128
70.4405-0.00630.16791.26591.70462.36570.0131-0.0245-0.0554-0.1169-0.21330.072-0.1099-0.05890.20020.03040.0526-0.02620.016-0.1086-0.09617.0548.54226.507
89.5437-6.5614-1.82967.77885.45756.9540.09670.01940.2554-0.7368-0.0716-0.0971-0.79750.4654-0.02510.12030.0175-0.0211-0.0422-0.0289-0.163212.12412.96120.752
90.59170.81021.38852.53872.67453.67660.22270.05990.12020.3542-0.13110.08660.37890.1166-0.09160.07790.0122-0.0133-0.0067-0.0729-0.140914.1567.69536.883
104.1297-0.5405-0.0143.3875-0.8391.3503-0.2649-0.3799-0.1830.60910.34431.0176-0.19250.0175-0.07930.10380.06870.112-0.024-0.00530.00056.007-13.03629.423
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 46
2X-RAY DIFFRACTION2A47 - 74
3X-RAY DIFFRACTION3A75 - 88
4X-RAY DIFFRACTION4A89 - 125
5X-RAY DIFFRACTION5A126 - 134
6X-RAY DIFFRACTION6A135 - 165
7X-RAY DIFFRACTION7A166 - 199
8X-RAY DIFFRACTION8A200 - 214
9X-RAY DIFFRACTION9A238 - 274
10X-RAY DIFFRACTION10B1 - 14
11X-RAY DIFFRACTION10C4 - 16

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