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- PDB-1n39: Structural and biochemical exploration of a critical amino acid i... -

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Basic information

Entry
Database: PDB / ID: 1n39
TitleStructural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase
Components
  • DNA complement strand
  • DNA inhibitor strand
  • N-glycosylase/DNA lyase
Keywordshydrolase / lyase/DNA / HhH-GPD / DNA-repair / glycosylase / oxoguanine / lyase-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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsNorman, D.P. / Chung, S.J. / Verdine, G.L.
CitationJournal: Biochemistry / Year: 2003
Title: Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase
Authors: Norman, D.P. / Chung, S.J. / Verdine, G.L.
History
DepositionOct 25, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 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 1.4Feb 14, 2024Group: 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
B: DNA complement strand
C: DNA inhibitor strand
A: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7344
Polymers44,6943
Non-polymers401
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.366, 92.366, 211.277
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: DNA chain DNA complement strand


Mass: 4635.010 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA inhibitor strand


Mass: 4396.838 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein N-glycosylase/DNA lyase / E.C.3.2.2.-, E.C.4.2.99.18 / hOgg1 glycosylase / 8-oxoguanosine DNA glycosylase/DNA-(apurinic or apyrimidinic site) lyase


Mass: 35662.332 Da / Num. of mol.: 1 / Mutation: D268E
Source method: isolated from a genetically manipulated source
Details: D268E form of hOgg1 bound to abasic THF inhibitor / Source: (gene. exp.) Homo sapiens (human) / Gene: HOGG1 / Plasmid: pet30a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O15527, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase
#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.: 153 / 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: 2.88 Å3/Da / Density % sol: 57.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 16-18% PEG 8000, 200mM Ca(OAC)2, 100mM sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2calcium acetate11
3sodium cacodylate11
4PEG 800012
5calcium acetate12
Crystal grow
*PLUS
Temperature: 4 ℃ / Details: Bruner, S.D., (2000) Nature, 403, 859.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMTris-HCl1drop
2100 mM1dropNaCl
31 mMEDTA1drop
410 mMdithiothreitol1drop
5100 mMsodium cacodylate1reservoir
6200 mMcalcium acetate1reservoir
717-18 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 9, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 34926 / Num. obs: 33215 / % possible obs: 95.1 % / Observed criterion σ(I): 1 / Redundancy: 5.05 % / Biso Wilson estimate: 30.3 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 22.3
Reflection shellResolution: 2.2→2.34 Å / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 5.6 / % possible all: 92.4
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 167899
Reflection shell
*PLUS
Highest resolution: 2.2 Å / % possible obs: 92.4 %

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FN7

1fn7


Resolution: 2.2→29.07 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1294 4.8 %RANDOM
Rwork0.242 ---
obs0.242 26745 95.9 %-
all-27897 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.2956 Å2 / ksol: 0.350117 e/Å3
Displacement parametersBiso mean: 52 Å2
Baniso -1Baniso -2Baniso -3
1-5.08 Å24.21 Å20 Å2
2--5.08 Å20 Å2
3----10.15 Å2
Refine analyzeLuzzati coordinate error free: 0.39 Å / Luzzati sigma a free: 0.4 Å
Refinement stepCycle: LAST / Resolution: 2.2→29.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2440 598 1 153 3192
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d20.8
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_mcbond_it1.291.5
X-RAY DIFFRACTIONc_mcangle_it2.152
X-RAY DIFFRACTIONc_scbond_it1.832
X-RAY DIFFRACTIONc_scangle_it2.82.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.342 202 4.8 %
Rwork0.331 3973 -
obs--92.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM
X-RAY DIFFRACTION4ION.PARAM
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.94
LS refinement shell
*PLUS
Rfactor Rfree: 0.33 / Rfactor Rwork: 0.31

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