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- PDB-1yqk: Human 8-oxoguanine glycosylase crosslinked with guanine containing DNA -

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Basic information

Entry
Database: PDB / ID: 1yqk
TitleHuman 8-oxoguanine glycosylase crosslinked with guanine containing DNA
Components
  • 5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*G)-3'
  • 5'-D(P*CP*AP*GP*GP*TP*CP*TP*AP*C)-3'
  • N-glycosylase/DNA lyase
KeywordsHYDROLASE/DNA / Disulfide crosslink / DNA glycosylase / undamaged DNA / HYDROLASE-DNA COMPLEX
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 / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / base-excision repair, AP site formation / depyrimidination / oxidized purine nucleobase lesion DNA N-glycosylase activity / 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 / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / base-excision repair, AP site formation / depyrimidination / oxidized purine nucleobase lesion DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / 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 / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / cellular response to cadmium ion / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / DNA-(apurinic or apyrimidinic site) lyase / nucleotide-excision repair / base-excision repair / response to radiation / nuclear matrix / response to estradiol / microtubule binding / endonuclease activity / response to ethanol / response to oxidative stress / damaged DNA binding / mitochondrial matrix / nuclear speck / response to xenobiotic stimulus / DNA damage response / regulation of DNA-templated transcription / negative regulation of apoptotic process / 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: 2.5 Å
AuthorsBanerjee, A. / Yang, W. / Karplus, M. / Verdine, G.L.
CitationJournal: Nature / Year: 2005
Title: Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA.
Authors: Banerjee, A. / Yang, W. / Karplus, M. / Verdine, G.L.
History
DepositionFeb 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: 5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*G)-3'
C: 5'-D(P*CP*AP*GP*GP*TP*CP*TP*AP*C)-3'
A: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2345
Polymers42,1023
Non-polymers1322
Water93752
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.358, 92.358, 211.312
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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DNA chain , 2 types, 2 molecules BC

#1: DNA chain 5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*G)-3'


Mass: 3414.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: yes
#2: DNA chain 5'-D(P*CP*AP*GP*GP*TP*CP*TP*AP*C)-3'


Mass: 2715.799 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: yes

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Protein , 1 types, 1 molecules A

#3: Protein N-glycosylase/DNA lyase


Mass: 35971.746 Da / Num. of mol.: 1 / Fragment: 8-oxoguanine DNA glycosylase / Mutation: N149C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OGG1 / Plasmid: pET30a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21(DE3)
References: UniProt: O15527, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds

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Non-polymers , 3 types, 54 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.19 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.936 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 17, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.936 Å / Relative weight: 1
ReflectionResolution: 2.5→29.06 Å / Num. all: 19210 / Num. obs: 17212 / % possible obs: 89.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 35.3 Å2
Reflection shellResolution: 2.5→2.59 Å / % possible all: 79.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→29.06 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 727095.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27 689 4 %RANDOM
Rwork0.235 ---
obs0.235 17212 89.5 %-
all-19210 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.894 Å2 / ksol: 0.357834 e/Å3
Displacement parametersBiso mean: 56.8 Å2
Baniso -1Baniso -2Baniso -3
1-6.12 Å210.42 Å20 Å2
2--11.82 Å20 Å2
3----17.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2414 410 7 52 2883
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_mcbond_it1.391.5
X-RAY DIFFRACTIONc_mcangle_it2.332
X-RAY DIFFRACTIONc_scbond_it7.292
X-RAY DIFFRACTIONc_scangle_it9.72.5
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.353 55 3.7 %
Rwork0.332 1415 -
obs--79.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMCHES
X-RAY DIFFRACTION4CHESWATER.TOP
X-RAY DIFFRACTION5ION.PARAMDNA-RNA.TOP

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