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- PDB-3go8: MutM encountering an intrahelical 8-oxoguanine (oxoG) lesion in E... -

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Basic information

Entry
Database: PDB / ID: 3go8
TitleMutM encountering an intrahelical 8-oxoguanine (oxoG) lesion in EC3-loop deletion complex
Components
  • 5'-D(*GP*CP*GP*TP*CP*CP*(8OG)P*GP*AP*TP*CP*TP*AP*C)-3'
  • 5'-D(P*GP*GP*TP*AP*GP*AP*TP*CP*CP*GP*GP*AP*CP*G)-3'
  • Formamidopyrimidine-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 / double-stranded DNA binding / 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. / Formamidopyrimidine-DNA glycosylase H2TH domain / MutM-like, N-terminal / 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. / Formamidopyrimidine-DNA glycosylase H2TH domain / MutM-like, N-terminal / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.89 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 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 2.0Feb 6, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary
Category: chem_comp / entity ...chem_comp / entity / entity_name_com / entity_src_gen / ndb_struct_na_base_pair_step / pdbx_entity_src_syn / struct_ref / struct_ref_seq_dif
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _ndb_struct_na_base_pair_step.helical_twist / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _struct_ref.db_code / _struct_ref.pdbx_seq_one_letter_code
Revision 2.1Oct 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Sep 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: Formamidopyrimidine-DNA glycosylase
B: 5'-D(P*GP*GP*TP*AP*GP*AP*TP*CP*CP*GP*GP*AP*CP*G)-3'
C: 5'-D(*GP*CP*GP*TP*CP*CP*(8OG)P*GP*AP*TP*CP*TP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7354
Polymers38,6703
Non-polymers651
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-17 kcal/mol
Surface area14900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.244, 92.655, 105.246
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 Formamidopyrimidine-DNA glycosylase / Fapy-DNA glycosylase / DNA-(apurinic or apyrimidinic site) lyase MutM / AP lyase MutM


Mass: 28855.496 Da / Num. of mol.: 1 / Fragment: MutM / Mutation: Q166C, deletion of 220-235
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: mutM, fpg / Plasmid: pET24B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) PlysS
References: UniProt: P84131, DNA-formamidopyrimidine glycosylase, DNA-(apurinic or apyrimidinic site) lyase
#2: DNA chain 5'-D(P*GP*GP*TP*AP*GP*AP*TP*CP*CP*GP*GP*AP*CP*G)-3'


Mass: 4948.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic DNA / Source: (synth.) synthetic construct (others)
#3: DNA chain 5'-D(*GP*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 / Details: synthetic DNA / Source: (synth.) synthetic construct (others)
#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.: 244 / 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: 2.94 Å3/Da / Density % sol: 58.21 %
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, VAPOR DIFFUSION, HANGING DROP
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: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 17, 2006
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. obs: 35790 / % possible obs: 98.7 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.101 / Χ2: 1.07 / Net I/σ(I): 15.897
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.89-1.965.50.4935551.0951100
1.96-2.045.60.36835451.0961100
2.04-2.135.60.27935711.0941100
2.13-2.245.60.21435861.0931100
2.24-2.385.60.17936021.0751100
2.38-2.575.60.15435921.0511100
2.57-2.825.60.13136031.045199.8
2.82-3.235.60.09835651.058198.1
3.23-4.075.60.07235531.039196.6
4.07-505.70.06336181.053193.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
CNSphasing
RefinementStarting model: 2F5O protein part only

2f5o


Resolution: 1.89→32.38 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.078 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1685 5 %RANDOM
Rwork0.185 ---
obs0.187 34033 95.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 114.58 Å2 / Biso mean: 28.86 Å2 / Biso min: 9.85 Å2
Refinement stepCycle: LAST / Resolution: 1.89→32.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1963 575 1 244 2783
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222673
X-RAY DIFFRACTIONr_angle_refined_deg1.3472.2513740
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4535254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.73121.02388
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.90515344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8861527
X-RAY DIFFRACTIONCHIRAL-CENTER RESTRAINTS (A''3)0.0820.2418
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021843
X-RAY DIFFRACTIONr_nbd_refined0.1910.21080
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21748
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2253
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.140.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.218
X-RAY DIFFRACTIONMAIN-CHAIN BOND REFINED ATOMS (A''2)0.7411.51304
X-RAY DIFFRACTIONMAIN-CHAIN ANGLE REFINED ATOMS (A''2)1.16822054
X-RAY DIFFRACTIONSIDE-CHAIN BOND REFINED ATOMS (A''2)1.69331752
X-RAY DIFFRACTIONSIDE-CHAIN ANGLE REFINED ATOMS (A''2)2.6314.51686
LS refinement shellResolution: 1.891→1.94 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 108 -
Rwork0.182 2156 -
all-2264 -
obs--86.38 %
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)
11.09440.1733-0.23521.23470.32370.97980.0095-0.1070.02860.0335-0.0239-0.1542-0.00510.11860.0143-0.0475-0.0213-0.0189-0.0187-0.0141-0.039321.472-12.8039.766
20.78610.245-0.25461.06050.48840.50210.0360.0039-0.0139-0.0337-0.0775-0.0105-0.0569-0.08510.0415-0.01340.0106-0.0219-0.0131-0.0159-0.026313.504-14.9445.071
31.0865-0.3505-0.65190.23520.2250.4005-0.0049-0.14990.03840.02220.039-0.05040.02450.0666-0.0341-0.02470.01590.00490.0376-0.0282-0.032225.131-18.22912.698
40.9611-0.04870.99870.1170.39552.7762-0.0282-0.02580.03230.02830.02280.14370.0850.05080.00540.01590.00370.01140.0056-0.0252-0.055313.414-15.62313.678
54.9283-0.42871.54634.90865.475810.12260.30730.12110.2195-0.0101-0.68680.35210.2548-0.54560.3795-0.05140.0455-0.03440.0199-0.1051-0.0172.822-9.1726.829
60.56850.0921-0.14681.02540.88631.74570.07930.039-0.0071-0.0343-0.15450.0916-0.0272-0.04590.0752-0.01970.0406-0.0209-0.0362-0.0717-0.01154.9097.88922.808
711.3615-6.4383-2.98566.15642.71441.20150.10140.12520.3498-0.4219-0.0706-0.3251-0.25730.0225-0.03080.03260.00440.0338-0.0645-0.0182-0.012714.1812.27720.008
82.26542.1530.30132.90070.45953.8708-0.07390.1511-0.02480.03560.234-0.24230.20920.4609-0.1601-0.00050.0277-0.0198-0.0097-0.0504-0.047520.0878.17535.125
91.61181.30061.99762.05832.33172.9893-0.0133-0.01230.09240.2936-0.06330.15270.2632-0.00310.07650.0288-0.04650.0167-0.0308-0.0558-0.038511.1167.49337.537
104.0861-0.91680.08452.5822-0.06190.0025-0.2477-0.5239-0.10040.49110.29860.5418-0.05310.1705-0.05090.03370.05490.08570.038-0.0053-0.04025.602-13.53930.316
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 33
2X-RAY DIFFRACTION2A34 - 73
3X-RAY DIFFRACTION3A74 - 108
4X-RAY DIFFRACTION4A109 - 123
5X-RAY DIFFRACTION5A124 - 133
6X-RAY DIFFRACTION6A134 - 200
7X-RAY DIFFRACTION7A201 - 216
8X-RAY DIFFRACTION8A238 - 251
9X-RAY DIFFRACTION9A252 - 274
10X-RAY DIFFRACTION10B2 - 15
11X-RAY DIFFRACTION10C2 - 15

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