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Yorodumi- PDB-1m3q: Crystal Structure of hogg1 D268E Mutant with Base-Excised DNA and... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m3q | ||||||
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Title | Crystal Structure of hogg1 D268E Mutant with Base-Excised DNA and 8-aminoguanine | ||||||
Components |
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Keywords | HYDROLASE/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 / 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å | ||||||
Authors | Chung, S.J. / Verdine, G.L. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m3q.cif.gz | 97.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m3q.ent.gz | 69.5 KB | Display | PDB format |
PDBx/mmJSON format | 1m3q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1m3q_validation.pdf.gz | 465.4 KB | Display | wwPDB validaton report |
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Full document | 1m3q_full_validation.pdf.gz | 471.7 KB | Display | |
Data in XML | 1m3q_validation.xml.gz | 17 KB | Display | |
Data in CIF | 1m3q_validation.cif.gz | 24.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m3/1m3q ftp://data.pdbj.org/pub/pdb/validation_reports/m3/1m3q | HTTPS FTP |
-Related structure data
Related structure data | 1m3hC 1ebmS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-DNA chain , 2 types, 2 molecules BC
#1: DNA chain | Mass: 4635.010 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 4412.837 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Protein , 1 types, 1 molecules A
#3: Protein | 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 / |
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#5: Chemical | ChemComp-ANG / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.42 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 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 |
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Crystal grow | *PLUS Temperature: 4, 20 ℃ / pH: 7.4 / Method: vapor diffusion, hanging dropDetails: protein:DNA=1:1.5, Bruner, S.D., (2000) Nature, 403, 859. | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.95 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 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
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.0295 Å2 / ksol: 0.367594 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→37.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 10 % / Rfactor Rfree: 0.268 / Rfactor Rwork: 0.234 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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