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

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Basic information

Entry
Database: PDB / ID: 3gpu
TitleMutM encountering an intrahelical 8-oxoguanine (oxoG) lesion in EC4-loop deletion complex
Components
  • DNA (5'-D(*AP*GP*GP*TP*AP*GP*AP*CP*TP*CP*GP*GP*AP*CP*GP*C)-3')
  • DNA (5'-D(*TP*GP*CP*GP*TP*CP*CP*(8OG)P*AP*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 / 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: 1.62 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 1.4Sep 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(*AP*GP*GP*TP*AP*GP*AP*CP*TP*CP*GP*GP*AP*CP*GP*C)-3')
C: DNA (5'-D(*TP*GP*CP*GP*TP*CP*CP*(8OG)P*AP*GP*TP*CP*TP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6924
Polymers38,6273
Non-polymers651
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-18 kcal/mol
Surface area14450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.218, 93.294, 104.972
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: 28812.473 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*TP*CP*GP*GP*AP*CP*GP*C)-3')


Mass: 4948.217 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*TP*GP*CP*GP*TP*CP*CP*(8OG)P*AP*GP*TP*CP*TP*AP*CP*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.: 287 / 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: 2.87 Å3/Da / Density % sol: 57.08 %
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: X25 / Wavelength: 1.1 Å
DetectorType: ADSC / Detector: CCD / Date: Aug 13, 2005
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.62→50 Å / Num. obs: 56204 / % possible obs: 97.9 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.056 / Χ2: 1.037 / Net I/σ(I): 25.882
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.62-1.6850.49556181.031199.4
1.68-1.755.50.34956331.048199.9
1.75-1.825.20.25356501.045199.3
1.82-1.925.20.17356171.049199.1
1.92-2.045.40.1256591.047199.4
2.04-2.25.30.08456391.009198.8
2.2-2.425.50.06556491.042198.7
2.42-2.775.40.06355961.052197.5
2.77-3.495.50.05256161.051196.3
3.49-505.40.03455270.994191

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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 2F5O, protein part only

2f5o


Resolution: 1.62→45.74 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.953 / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.049 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.204 2748 5.1 %RANDOM
Rwork0.188 ---
obs0.189 54101 96.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.56 Å2 / Biso mean: 26.277 Å2 / Biso min: 10.51 Å2
Refinement stepCycle: LAST / Resolution: 1.62→45.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1962 515 1 287 2765
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222616
X-RAY DIFFRACTIONr_angle_refined_deg1.3332.2283649
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5375255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.78320.77890
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.56815348
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5931529
LS refinement shellResolution: 1.62→1.662 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 198 -
Rwork0.219 3477 -
all-3675 -
obs--88.83 %
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)
10.98140.0526-0.36541.37190.44971.43580.0109-0.11040.04820.0064-0.0056-0.0966-0.03620.0987-0.0053-0.0342-0.0077-0.0093-0.0117-0.0092-0.063221.148-13.1439.777
20.72930.0446-0.1061.39680.6520.81810.04550.00340.0233-0.0338-0.06730.028-0.0455-0.090.0217-0.00470.0093-0.0071-0.0072-0.0127-0.045513.463-14.94.881
31.0365-0.4988-0.50950.73040.35810.5519-0.0088-0.14560.03660.09820.0346-0.05140.02450.105-0.02570.02070.0060.00820.0194-0.0128-0.06324.945-18.11613.091
40.02150.04770.05021.0891.2651.47080.0105-0.01150.0099-0.2021-0.220.1423-0.0634-0.20260.2095-0.00620.0203-0.01950.0249-0.0525-0.03215.933-3.7312.263
50.7644-0.11660.04911.39731.31012.55030.07340.05930.00480.05-0.18570.11090.0765-0.10910.1123-0.00950.0107-0.0036-0.0259-0.076-0.03595.8637.57826.152
613.5251-6.5155-2.67346.972.86652.6540.30410.1770.3453-0.5178-0.2252-0.3681-0.4260.0927-0.0790.05350.00750.0226-0.0563-0.0133-0.068213.23612.53719.821
71.22071.37441.20923.03312.27322.46580.1210.0084-0.00080.2908-0.0685-0.01550.24170.0422-0.05250.0408-0.0051-0.0033-0.0345-0.0398-0.068614.757.96136.528
83.2968-0.3157-0.01022.2407-0.35150.7723-0.1248-0.31710.02240.35120.11720.5210.0165-0.07180.00760.04870.00570.0735-0.0086-0.0411-0.02383.723-12.54428.182
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 34
2X-RAY DIFFRACTION2A35 - 73
3X-RAY DIFFRACTION3A74 - 110
4X-RAY DIFFRACTION4A111 - 154
5X-RAY DIFFRACTION5A155 - 199
6X-RAY DIFFRACTION6A200 - 216
7X-RAY DIFFRACTION7A239 - 274
8X-RAY DIFFRACTION8B2 - 14
9X-RAY DIFFRACTION8C4 - 15

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