[English] 日本語
![](img/lk-miru.gif)
- PDB-1e9n: A second divalent metal ion in the active site of a new crystal f... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1e9n | ||||||
---|---|---|---|---|---|---|---|
Title | A second divalent metal ion in the active site of a new crystal form of human apurinic/apyrimidinic endonuclease, Ape1, and its implications for the catalytic mechanism | ||||||
![]() | DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE | ||||||
![]() | DNA REPAIR / DNA REPAIR ENDONUCLEASE / BASE EXCISION REPAIR / ABASIC ENDONUCLEASE / APE1 / HAP1 / REF-1 / ALPHA / BETA SANDWICH | ||||||
Function / homology | ![]() Resolution of Abasic Sites (AP sites) / class II DNA-(apurinic or apyrimidinic site) endonuclease activity / phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands / telomere maintenance via base-excision repair / site-specific endodeoxyribonuclease activity, specific for altered base / DNA-(abasic site) binding / double-stranded DNA exodeoxyribonuclease activity / double-stranded telomeric DNA binding / double-stranded DNA 3'-5' DNA exonuclease activity / phosphodiesterase I activity ...Resolution of Abasic Sites (AP sites) / class II DNA-(apurinic or apyrimidinic site) endonuclease activity / phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands / telomere maintenance via base-excision repair / site-specific endodeoxyribonuclease activity, specific for altered base / DNA-(abasic site) binding / double-stranded DNA exodeoxyribonuclease activity / double-stranded telomeric DNA binding / double-stranded DNA 3'-5' DNA exonuclease activity / phosphodiesterase I activity / exodeoxyribonuclease III / positive regulation of gene expression via chromosomal CpG island demethylation / Displacement of DNA glycosylase by APEX1 / phosphoric diester hydrolase activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / uracil DNA N-glycosylase activity / DNA catabolic process / 3'-5'-DNA exonuclease activity / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / POLB-Dependent Long Patch Base Excision Repair / PCNA-Dependent Long Patch Base Excision Repair / DNA-(apurinic or apyrimidinic site) endonuclease activity / regulation of mRNA stability / 3'-5' exonuclease activity / telomere maintenance / base-excision repair, gap-filling / cell redox homeostasis / DNA endonuclease activity / base-excision repair / chromatin DNA binding / transcription corepressor activity / RNA-DNA hybrid ribonuclease activity / endonuclease activity / DNA recombination / regulation of apoptotic process / damaged DNA binding / chromosome, telomeric region / transcription coactivator activity / oxidoreductase activity / ribosome / nuclear speck / DNA repair / centrosome / nucleolus / perinuclear region of cytoplasm / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / RNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Beernink, P.T. / Segelke, B.W. / Rupp, B. | ||||||
![]() | ![]() Title: Two Divalent Metal Ions in the Active Site of a New Crystal Form of Human Apurinic/Apyrimidinic Endonuclease, Ape1: Implications for the Catalytic Mechanism Authors: Beernink, P.T. / Segelke, B.W. / Hadi, M.Z. / Erzberger, J.P. / Wilson III, D.M. / Rupp, B. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 129 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 99.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
2 | ![]()
| ||||||||||||
Unit cell |
| ||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
| ||||||||||||
Details | THE BIOLOGICAL UNIT IS HALF OF THE ASYMMETRIC UNIT |
-
Components
#1: Protein | Mass: 35606.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P27695, DNA-(apurinic or apyrimidinic site) lyase #2: Chemical | ChemComp-PB / #3: Water | ChemComp-HOH / | Compound details | ENDONUCLEO | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 53 % | |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: HANGING DROP, DROP 2+2 UL, 15MG/ML PROTEIN, 1 ML WELL, 0.1M TRIS-HCL, PH 7.5, 0.2M NAOAC, 30% PEG4K, 20MM HECAMEG, 1MM PB(OAC)2, 1MM DTT | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 15, 1999 / Details: DUAL CRYSTAL MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2398 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→67.42 Å / Num. obs: 34905 / % possible obs: 93 % / Redundancy: 2.9 % / Rsym value: 0.082 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 2 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 2.1 / % possible all: 70.5 |
Reflection | *PLUS Highest resolution: 2.2 Å / Num. measured all: 102875 / Rmerge(I) obs: 0.082 |
Reflection shell | *PLUS % possible obs: 70.5 % |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: TO BE PUBLISHED Resolution: 2.2→20 Å / Isotropic thermal model: TNT BCORREL V1.0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTGEO_V012 / Details: NCS WEIGHT 60, THEN RELAXED AT END OF REFINEMENT
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: BABENET SCALING / Bsol: 150 Å2 / ksol: 0.8 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: TNT / Version: 5F / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection Rfree: 3499 / Rfactor all: 0.186 / Rfactor Rfree: 0.252 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|