[English] 日本語

- PDB-1emh: CRYSTAL STRUCTURE OF HUMAN URACIL-DNA GLYCOSYLASE BOUND TO UNCLEA... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1emh | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF HUMAN URACIL-DNA GLYCOSYLASE BOUND TO UNCLEAVED SUBSTRATE-CONTAINING DNA | ||||||
![]() |
| ||||||
![]() | hydrolase/DNA / alpha/beta fold / Uracil-DNA Glycosylase / protein/DNA / hydrolase-DNA COMPLEX | ||||||
Function / homology | ![]() base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / depyrimidination / Displacement of DNA glycosylase by APEX1 / single strand break repair / isotype switching / uracil DNA N-glycosylase activity / ribosomal small subunit binding / somatic hypermutation of immunoglobulin genes / Recognition and association of DNA glycosylase with site containing an affected pyrimidine ...base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / depyrimidination / Displacement of DNA glycosylase by APEX1 / single strand break repair / isotype switching / uracil DNA N-glycosylase activity / ribosomal small subunit binding / somatic hypermutation of immunoglobulin genes / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Chromatin modifications during the maternal to zygotic transition (MZT) / base-excision repair / damaged DNA binding / negative regulation of apoptotic process / mitochondrion / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Parikh, S.S. / Slupphaug, G. / Krokan, H.E. / Blackburn, G.M. / Tainer, J.A. | ||||||
![]() | ![]() Title: Uracil-DNA glycosylase-DNA substrate and product structures: conformational strain promotes catalytic efficiency by coupled stereoelectronic effects. Authors: Parikh, S.S. / Walcher, G. / Jones, G.D. / Slupphaug, G. / Krokan, H.E. / Blackburn, G.M. / Tainer, J.A. #1: ![]() Title: Base excision repair initiation revealed by crystal structures and binding kinetics of human uracil-DNA glycosylase with DNA Authors: Parikh, S.S. / Mol, C.D. / Slupphaug, G. / Krokan, H.E. / Tainer, J.A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 73.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 51.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 380.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 381.3 KB | Display | |
Data in XML | ![]() | 6.4 KB | Display | |
Data in CIF | ![]() | 10.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-
Components
#1: DNA chain | Mass: 2697.768 Da / Num. of mol.: 1 / Source method: obtained synthetically |
---|---|
#2: DNA chain | Mass: 3070.071 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Protein | Mass: 25544.137 Da / Num. of mol.: 1 / Mutation: RESIDUES 85-304 Source method: isolated from a genetically manipulated source Details: MITOCHONDRIAL PROTEIN / Source: (gene. exp.) ![]() ![]() ![]() |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.22 % | |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 4000, HEPES buffer, NaCl, dioxane, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K | |||||||||||||||||||||||||||||||||||
Components of the solutions |
| |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC / Detector: CCD / Date: Aug 16, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 28501 / Num. obs: 26594 / % possible obs: 93 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 4.3 % / Biso Wilson estimate: 20.02 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 14.9 |
Reflection shell | Highest resolution: 1.8 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.231 / Num. unique all: 1636 / % possible all: 58 |
Reflection | *PLUS Num. measured all: 116160 |
Reflection shell | *PLUS % possible obs: 76.9 % |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
| |||||||||||||||||||||||||
Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.216 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |