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- PDB-1fn7: COUPLING OF DAMAGE RECOGNITION AND CATALYSIS BY A HUMAN BASE-EXCI... -

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Basic information

Entry
Database: PDB / ID: 1fn7
TitleCOUPLING OF DAMAGE RECOGNITION AND CATALYSIS BY A HUMAN BASE-EXCISION DNA REPAIR PROTEIN
Components
  • 8-OXOGUANINE DNA GLYCOSYLASE 1
  • DNA (5'-D(*GP*CP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*TP*AP*CP*C)-3')
  • DNA (5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3')
KeywordsHYDROLASE/DNA / DNA REPAIR / DNA GLYCOSYLASE / PROTEIN/DNA / Helix hairpin helix / base recognition / oxoguanine / hydroxyguanine / base flipping / flipped-out base / extrahelical DNA / mechanism-based inhibitor / base-exicision repair / AP lyase / DNA glycosidase / 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 / oxidized purine nucleobase lesion DNA N-glycosylase activity / base-excision repair, AP site formation / depyrimidination / 8-oxo-7,8-dihydroguanine 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 / oxidized purine nucleobase lesion DNA N-glycosylase activity / base-excision repair, AP site formation / depyrimidination / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / positive regulation of gene expression via chromosomal CpG island demethylation / oxidized purine DNA binding / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / cellular response to reactive oxygen species / nucleotide-excision repair / response to radiation / base-excision repair / nuclear matrix / response to oxidative stress / endonuclease activity / microtubule binding / damaged DNA binding / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / mitochondrial matrix / DNA damage response / regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / 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 ...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 / Endonuclease III; domain 1 / DNA glycosylase / 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 / Resolution: 2.6 Å
AuthorsNorman, D.P.G. / Bruner, S.D. / Verdine, G.L.
Citation
Journal: J.Am.Chem.Soc. / Year: 2001
Title: Coupling of substrate recognition and catalysis by a human base-excision DNA repair protein.
Authors: Norman, D.P. / Bruner, S.D. / Verdine, G.L.
#1: Journal: Nature / Year: 2000
Title: Structural basis for recognition and repair of the endogenous mutagen 8-oxoguanine in DNA
Authors: Bruner, S.D. / Norman, D.P.G. / Verdine, G.L.
History
DepositionAug 21, 2000Deposition site: NDB / Processing site: NDB
Revision 1.0Apr 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3')
D: DNA (5'-D(*GP*CP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*TP*AP*CP*C)-3')
A: 8-OXOGUANINE DNA GLYCOSYLASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7204
Polymers44,6803
Non-polymers401
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.113, 92.113, 211.014
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Cell settinghexagonal
Space group name H-MP6522

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Components

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


Mass: 4635.010 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*GP*CP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*TP*AP*CP*C)-3')


Mass: 4396.838 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein 8-OXOGUANINE DNA GLYCOSYLASE 1 / E.C.3.2.2.- / HOGG1 / DNA GLYCOSYLASE/AP LYASE


Mass: 35648.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET30A-TRUNC.HOGG1 / Production host: Escherichia coli (E. coli)
References: UniProt: O15527, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM sodium cacodylate pH 6.5, 200 mM calcium acetate, 16-18% PEG, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium cacodylate11
2calcium acetate11
3PEG11
4PEG12
Crystal grow
*PLUS
pH: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mMTris-HCl1drop
250 mM1dropNaCl
31 mMEDTA1drop
45 mMbeta-mercaptoethanol1drop
5100 mMsodium cacodylate1reservoir
6200 mMcalcium acetate1reservoir
716-18 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332
DetectorType: SBC-1 / Detector: CCD / Date: Mar 7, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 18214 / Num. obs: 17653 / % possible obs: 96.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 4.74 % / Biso Wilson estimate: 35.4 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 14.3
Reflection shellResolution: 2.54→2.69 Å / Redundancy: 3.15 % / Rmerge(I) obs: 0.352 / Num. unique all: 1757 / % possible all: 99.8
Reflection
*PLUS
Num. measured all: 83683
Reflection shell
*PLUS
% possible obs: 99.8 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.6→29.85 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 294195.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1
Details: conformation of the abasic deoxyribose ring was determined by modeling it as RNA (C3'-endo) and DNA (C2'-endo), and performing simulated annealing on both models. When modeled in the C2'- ...Details: conformation of the abasic deoxyribose ring was determined by modeling it as RNA (C3'-endo) and DNA (C2'-endo), and performing simulated annealing on both models. When modeled in the C2'-endo conformation, R and Rfree were lower, and the model fit the experimental Fo-Fc omit density better
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1505 10.1 %RANDOM
Rwork0.221 ---
obs0.221 14841 87 %-
all-17058 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.06 Å2 / ksol: 0.339 e/Å3
Displacement parametersBiso mean: 40.6 Å2
Baniso -1Baniso -2Baniso -3
1-4.05 Å26.93 Å20 Å2
2--4.05 Å20 Å2
3----8.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.6→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2440 598 1 132 3171
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d20.7
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it1.151.5
X-RAY DIFFRACTIONc_mcangle_it1.982
X-RAY DIFFRACTIONc_scbond_it1.462
X-RAY DIFFRACTIONc_scangle_it2.32.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.361 175 9.1 %
Rwork0.264 1752 -
obs--69.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PADNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9

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