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

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Basic information

Entry
Database: PDB / ID: 3gpp
TitleMutM encountering an intrahelical 8-oxoguanine (oxoG) lesion in EC3-T224P complex
Components
  • DNA (5'-D(P*CP*GP*TP*CP*CP*(8OG)P*GP*AP*TP*CP*TP*AP*C)-3')
  • DNA (5'-D(P*GP*GP*TP*AP*GP*AP*TP*CP*CP*GP*GP*AP*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 / 8-oxo-7,8-dihydroguanine 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: 2.15 Å
AuthorsSpong, M.C. / 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 1.4Sep 6, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: DNA glycosylase
B: DNA (5'-D(P*GP*GP*TP*AP*GP*AP*TP*CP*CP*GP*GP*AP*C)-3')
C: DNA (5'-D(P*CP*GP*TP*CP*CP*(8OG)P*GP*AP*TP*CP*TP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4594
Polymers40,3943
Non-polymers651
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-18 kcal/mol
Surface area14510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.243, 93.841, 103.405
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: 30579.342 Da / Num. of mol.: 1 / Mutation: Q166C, T224P
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(P*GP*GP*TP*AP*GP*AP*TP*CP*CP*GP*GP*AP*C)-3')


Mass: 4948.217 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(P*CP*GP*TP*CP*CP*(8OG)P*GP*AP*TP*CP*TP*AP*C)-3')


Mass: 4866.141 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


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.72 Å3/Da / Density % sol: 54.73 %
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: NSLS / Beamline: X29A / Wavelength: 0.98 Å
DetectorType: ADSC / Detector: CCD / Date: Apr 3, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 24531 / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.08 / Χ2: 1.031 / Net I/σ(I): 17.988
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.15-2.236.70.55323770.979199.9
2.23-2.326.90.42624200.987199.9
2.32-2.426.90.33324101.0341100
2.42-2.556.90.23924191.021100
2.55-2.716.90.17424331.0141100
2.71-2.926.90.1224321.0211100
2.92-3.216.80.0824601.0811100
3.21-3.686.80.06824621.0351100
3.68-4.636.60.06424981.0491100
4.63-508.70.06426201.071198.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.4.0066refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
CNSphasing
RefinementStarting model: pdb entry 1R2Y, protein part only

1r2y


Resolution: 2.15→31.07 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.13 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.202 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1119 4.8 %RANDOM
Rwork0.196 ---
obs0.198 23314 95.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 197.15 Å2 / Biso mean: 55.58 Å2 / Biso min: 26.08 Å2
Refinement stepCycle: LAST / Resolution: 2.15→31.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1954 534 1 73 2562
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222593
X-RAY DIFFRACTIONr_angle_refined_deg1.3742.2393622
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4645249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.02621.14987
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.85915331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4221526
LS refinement shellResolution: 2.15→2.209 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 70 -
Rwork0.225 1424 -
all-1494 -
obs--87.47 %
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)
11.44550.09930.55722.5116-0.6692.33370.0339-0.2602-0.0842-0.0373-0.10640.18970.1244-0.25950.0726-0.2771-0.02490.04240.11790.0335-0.0209-22.08959.1138.95
26.29912.6015-3.03872.386-3.79646.39010.1942-0.41940.09160.3266-0.4128-0.4641-0.4324-0.02550.2185-0.1676-0.0301-0.04210.15440.0349-0.0467-9.28870.01111.602
30.9567-0.4690.39351.03-0.47411.1114-0.0692-0.1732-0.0647-0.0095-0.0093-0.02730.0398-0.05060.0785-0.19560.0133-0.00010.12770.0459-0.0349-20.3162.629.133
40.6488-0.4042-0.25182.682-2.67453.3967-0.0373-0.26890.18-0.5784-0.4271-0.17150.28820.52730.4644-0.21660.10080.03120.18170.1421-0.011-5.9650.79310.078
50.34960.1164-0.08182.0129-2.59773.76250.16350.16120.03460.0643-0.5004-0.15870.0170.2440.3369-0.20690.05710.04470.13520.2201-0.0181-4.93339.13924.932
624.2368-8.00976.28148.0949-8.64189.54130.2533-0.2151-0.7022-1.1858-0.07370.27130.6427-0.2659-0.1796-0.0270.04420.0055-0.00680.0251-0.0724-12.33233.91719.077
74.68345.6147-0.37579.7781-6.463412.14540.11760.46650.2897-0.15770.25811.0576-0.4312-0.7765-0.3757-0.1430.0910.01210.15130.131-0.0502-20.05737.35633.53
81.3152-0.481-0.34144.2188-3.75183.80590.1401-0.0631-0.09170.6315-0.4081-0.3069-0.47760.3650.2679-0.1035-0.0865-0.0580.11220.1346-0.0475-10.84638.98136.57
912.296-5.188-2.28818.2233-0.98671.7813-0.8396-1.74410.66881.32140.5516-1.6853-0.17760.50730.2881-0.07880.0562-0.27280.31950.06710.033-4.01859.31829.259
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 31
2X-RAY DIFFRACTION2A32 - 41
3X-RAY DIFFRACTION3A42 - 112
4X-RAY DIFFRACTION4A113 - 150
5X-RAY DIFFRACTION5A151 - 199
6X-RAY DIFFRACTION6A200 - 215
7X-RAY DIFFRACTION7A216 - 253
8X-RAY DIFFRACTION8A254 - 274
9X-RAY DIFFRACTION9B2 - 14
10X-RAY DIFFRACTION9C3 - 15

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