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- PDB-1m3q: Crystal Structure of hogg1 D268E Mutant with Base-Excised DNA and... -

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Basic information

Entry
Database: PDB / ID: 1m3q
TitleCrystal Structure of hogg1 D268E Mutant with Base-Excised DNA and 8-aminoguanine
Components
  • 5'-D(*GP*CP*GP*TP*CP*CP*AP*(DRZ)P*GP*TP*CP*TP*AP*CP*C)-3'
  • 5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3'
  • 8-oxoguanine DNA glycosylase
KeywordsHYDROLASE/DNA / 8-oxoguanine / DNA glycosylase / DNA repair / end product / hogg / 8-aminoguanine / re-ligation / 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 / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / DNA-(apurinic or apyrimidinic site) lyase / 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
8-AMINOGUANINE / DNA / DNA (> 10) / N-glycosylase/DNA lyase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsChung, S.J. / Verdine, G.L.
CitationJournal: Chem.Biol. / Year: 2004
Title: Structures of End Products Resulting from Lesion Processing by a DNA Glycosylase/Lyase
Authors: Chung, S.J. / Verdine, G.L.
History
DepositionJun 28, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2004Provider: 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_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_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 / 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: 5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3'
C: 5'-D(*GP*CP*GP*TP*CP*CP*AP*(DRZ)P*GP*TP*CP*TP*AP*CP*C)-3'
A: 8-oxoguanine DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9165
Polymers44,7103
Non-polymers2062
Water3,135174
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.415, 92.415, 211.425
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*GP*AP*CP*GP*C)-3'


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


Mass: 4412.837 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein , 1 types, 1 molecules A

#3: Protein 8-oxoguanine DNA glycosylase


Mass: 35662.332 Da / Num. of mol.: 1 / Fragment: core fragment (residues 12-325) / Mutation: d268e
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ogg1 / Production host: Escherichia coli (E. coli)
References: UniProt: O15527, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds

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Non-polymers , 3 types, 176 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-ANG / 8-AMINOGUANINE


Mass: 166.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6N6O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.89 Å3/Da / Density % sol: 57.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, calcium acetate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2calcium acetate11
3cacodylate11
Crystal grow
*PLUS
Temperature: 4, 20 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop
Details: protein:DNA=1:1.5, 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: 0.95 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 42940 / Num. obs: 42784 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 99.4 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.067
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.45 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.3 / Num. unique all: 4166 / % possible all: 99.1
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 42539 / % possible obs: 99.4 % / Redundancy: 5.2 %
Reflection shell
*PLUS
% possible obs: 99.1 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.3

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1EBM

1ebm


Resolution: 1.9→37.43 Å / Rfactor Rfree error: 0.004 / Data cutoff high rms absF: 287857.55 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2675 3828 10.1 %RANDOM
Rwork0.235 ---
all-42940 --
obs-37734 87.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.0295 Å2 / ksol: 0.367594 e/Å3
Displacement parametersBiso mean: 41.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.55 Å22.42 Å20 Å2
2--3.55 Å20 Å2
3----7.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.9→37.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2440 599 13 174 3226
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_d21.1
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it1.361.5
X-RAY DIFFRACTIONc_mcangle_it2.092
X-RAY DIFFRACTIONc_scbond_it1.892
X-RAY DIFFRACTIONc_scangle_it2.782.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.315 509 10.6 %
Rwork0.286 4283 -
obs--68.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5SJC_DSJC_D
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rfree: 0.268 / Rfactor Rwork: 0.234
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9

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