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- PDB-1m3q: Crystal Structure of hogg1 D268E Mutant with Base-Excised DNA and... -
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Open data
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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 | ||||||
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![]() | HYDROLASE/DNA / ![]() ![]() ![]() | ||||||
Function / homology | ![]() Defective OGG1 Substrate Binding / Defective OGG1 Substrate Processing / Defective OGG1 Localization / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chung, S.J. / Verdine, G.L. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 97.1 KB | Display | ![]() |
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PDB format | ![]() | 69.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1m3hC ![]() 1ebmS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() ![]() References: UniProt: O15527, ![]() |
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-Non-polymers , 3 types, 176 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/ANG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ANG.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-CA / |
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#5: Chemical | ChemComp-ANG / |
#6: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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![]() |
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 |
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Processing
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Refinement | Method to determine structure![]() ![]() 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![]() ![]() | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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