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- PDB-3ih7: Crystal structure of catalytically active human 8-oxoguanine glyc... -

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Basic information

Entry
Database: PDB / ID: 3ih7
TitleCrystal structure of catalytically active human 8-oxoguanine glycosylase distally crosslinked to guanine-containing DNA
Components
  • 5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3'
  • 5'-D(AP*TP*CP*TP*GP*GP*AP*CP*CP*TP*GP*CP*A)-3'
  • N-glycosylase/DNA lyase
Keywords(HYDROLASE / LYASE)/DNA / DISULFIDE CROSSLINK / DNA GLYCOSYLASE / UNDAMAGED DNA / LYASE)-DNA COMPLEX / DNA damage / DNA repair / Glycosidase / Hydrolase / Lyase / Mitochondrion / Multifunctional enzyme / Nucleus
Function / homology
Function and homology information


Defective OGG1 Substrate Binding / Defective OGG1 Substrate Processing / Defective OGG1 Localization / depurination / negative regulation of double-strand break repair via single-strand annealing / oxidized purine nucleobase lesion DNA N-glycosylase activity / base-excision repair, AP site formation / depyrimidination / positive regulation of gene expression via chromosomal CpG island demethylation / Displacement of DNA glycosylase by APEX1 ...Defective OGG1 Substrate Binding / Defective OGG1 Substrate Processing / Defective OGG1 Localization / depurination / negative regulation of double-strand break repair via single-strand annealing / oxidized purine nucleobase lesion DNA N-glycosylase activity / base-excision repair, AP site formation / depyrimidination / positive regulation of gene expression via chromosomal CpG island demethylation / Displacement of DNA glycosylase by APEX1 / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / response to folic acid / oxidized purine DNA binding / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / response to light stimulus / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / cellular response to cadmium ion / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / nucleotide-excision repair / response to radiation / base-excision repair / nuclear matrix / cellular response to reactive oxygen species / response to estradiol / microtubule binding / endonuclease activity / response to ethanol / response to oxidative stress / damaged DNA binding / nuclear speck / mitochondrial matrix / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA damage response / regulation of DNA-templated transcription / negative regulation of apoptotic process / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus / cytosol
Similarity search - Function
TATA-Binding Protein - #40 / 8-oxoguanine DNA-glycosylase / 8-oxoguanine DNA glycosylase, N-terminal / 8-oxoguanine DNA glycosylase, N-terminal domain / Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal) / Endonuclease Iii, domain 2 / Hypothetical protein; domain 2 / HhH-GPD superfamily base excision DNA repair protein / Helix-hairpin-helix, base-excision DNA repair, C-terminal / HhH-GPD domain ...TATA-Binding Protein - #40 / 8-oxoguanine DNA-glycosylase / 8-oxoguanine DNA glycosylase, N-terminal / 8-oxoguanine DNA glycosylase, N-terminal domain / Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal) / Endonuclease Iii, domain 2 / Hypothetical protein; domain 2 / HhH-GPD superfamily base excision DNA repair protein / Helix-hairpin-helix, base-excision DNA repair, C-terminal / HhH-GPD domain / endonuclease III / DNA glycosylase / Endonuclease III; domain 1 / TATA-Binding Protein / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / N-glycosylase/DNA lyase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsVerdine, G.L. / Crenshaw, C.M. / Oo, K.S. / Kutchukian, P.S.
CitationJournal: To be Published
Title: A Catalytic Checkpoint in Base Excision by the Human 8-Oxoguanine DNA Glycosylase hOGG1
Authors: Crenshaw, C.M. / Oo, K.S. / Kutchukian, P.S. / Verdine, G.L.
History
DepositionJul 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
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: N-glycosylase/DNA lyase
B: 5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3'
C: 5'-D(AP*TP*CP*TP*GP*GP*AP*CP*CP*TP*GP*CP*A)-3'


Theoretical massNumber of molelcules
Total (without water)43,9493
Polymers43,9493
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-13.8 kcal/mol
Surface area16860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.000, 91.000, 211.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsBiological unit is the same as asymmetric unit.

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Components

#1: Protein N-glycosylase/DNA lyase / 8-oxoguanine DNA glycosylase / DNA-(apurinic or apyrimidinic site) lyase / AP lyase


Mass: 35651.391 Da / Num. of mol.: 1 / Fragment: UNP residues 12-325 / Mutation: S292C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMH, MUTM, OGG1, OGH1 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: O15527, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase
#2: DNA chain 5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3'


Mass: 4345.829 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic DNA
#3: DNA chain 5'-D(AP*TP*CP*TP*GP*GP*AP*CP*CP*TP*GP*CP*A)-3'


Mass: 3951.586 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic DNA

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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: 57.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 63 mM Magnesium acetate, 12.6% PEG 8000, 90 mM Sodium cacodylate, 10 mM Sodium acetate pH 4.6, 60 mM Sodium fluoride, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1Magnesium acetate11
2PEG 800011
3Sodium cacodylate11
4Sodium acetate11
5Sodium fluoride11
6Magnesium acetate12
7PEG 800012
8Sodium cacodylate12
9Sodium acetate12
10Sodium fluoride12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
Details: Vertical and horizontal focusing mirrors in Kirkpatrick-Baez geometry
RadiationMonochromator: Cryogenically-cooled single crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. obs: 10527 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Rsym value: 0.134
Reflection shellResolution: 3.05→3.16 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.697 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIX1.4_162refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2NOL

2nol


Resolution: 3.1→32.19 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.28 / σ(F): 0.19 / Phase error: 25.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2673 492 5.26 %
Rwork0.2284 --
obs0.2305 9362 93.39 %
all-10500 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.618 Å2 / ksol: 0.323 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-10.1127 Å20 Å2-0 Å2
2--10.1127 Å20 Å2
3----20.2255 Å2
Refinement stepCycle: LAST / Resolution: 3.1→32.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2493 530 0 0 3023
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023156
X-RAY DIFFRACTIONf_angle_d0.5794401
X-RAY DIFFRACTIONf_dihedral_angle_d21.41169
X-RAY DIFFRACTIONf_chiral_restr0.038475
X-RAY DIFFRACTIONf_plane_restr0.002480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.41240.32011060.27712001X-RAY DIFFRACTION87
3.4124-3.90540.28961100.23072229X-RAY DIFFRACTION96
3.9054-4.91760.27131250.20872203X-RAY DIFFRACTION93
4.9176-32.19220.23921510.22332437X-RAY DIFFRACTION97
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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