+Open data
-Basic information
Entry | Database: PDB / ID: 2e6m | ||||||
---|---|---|---|---|---|---|---|
Title | structure of mouse werner exonuclease domain | ||||||
Components | Werner syndrome ATP-dependent helicase homolog | ||||||
Keywords | HYDROLASE / apo form | ||||||
Function / homology | Function and homology information Processive synthesis on the C-strand of the telomere / Removal of the Flap Intermediate from the C-strand / Homologous DNA Pairing and Strand Exchange / Presynaptic phase of homologous DNA pairing and strand exchange / Resolution of D-loop Structures through Holliday Junction Intermediates / 3'-flap-structured DNA binding / positive regulation of strand invasion / HDR through Single Strand Annealing (SSA) / telomeric G-quadruplex DNA binding / HDR through Homologous Recombination (HRR) ...Processive synthesis on the C-strand of the telomere / Removal of the Flap Intermediate from the C-strand / Homologous DNA Pairing and Strand Exchange / Presynaptic phase of homologous DNA pairing and strand exchange / Resolution of D-loop Structures through Holliday Junction Intermediates / 3'-flap-structured DNA binding / positive regulation of strand invasion / HDR through Single Strand Annealing (SSA) / telomeric G-quadruplex DNA binding / HDR through Homologous Recombination (HRR) / forked DNA-dependent helicase activity / G2/M DNA damage checkpoint / 8-hydroxy-2'-deoxyguanosine DNA binding / telomeric D-loop binding / Processing of DNA double-strand break ends / regulation of growth rate / G-quadruplex DNA unwinding / telomeric D-loop disassembly / Y-form DNA binding / DNA 3'-5' helicase / four-way junction helicase activity / MutLalpha complex binding / Regulation of TP53 Activity through Phosphorylation / bubble DNA binding / protein localization to nucleolus / response to UV-C / exonuclease activity / DNA metabolic process / 3'-5' DNA helicase activity / DNA synthesis involved in DNA repair / replication fork processing / DNA unwinding involved in DNA replication / replicative senescence / four-way junction DNA binding / isomerase activity / cellular response to starvation / 3'-5' exonuclease activity / DNA helicase activity / telomere maintenance / replication fork / determination of adult lifespan / double-strand break repair via homologous recombination / base-excision repair / cellular response to gamma radiation / cellular senescence / double-strand break repair / chromosome / manganese ion binding / regulation of apoptotic process / response to oxidative stress / DNA replication / chromosome, telomeric region / Hydrolases; Acting on ester bonds / nuclear speck / centrosome / chromatin binding / nucleolus / magnesium ion binding / protein homodimerization activity / ATP hydrolysis activity / nucleoplasm / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Cho, Y. / Choi, J.M. | ||||||
Citation | Journal: TO BE PUBLISHED Title: probing the roles of active site residues in 3'-5' exonuclease of werner syndrome protein Authors: Cho, Y. / Choi, J.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2e6m.cif.gz | 52.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2e6m.ent.gz | 36.6 KB | Display | PDB format |
PDBx/mmJSON format | 2e6m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/2e6m ftp://data.pdbj.org/pub/pdb/validation_reports/e6/2e6m | HTTPS FTP |
---|
-Related structure data
Related structure data | 2e6lSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 23401.854 Da / Num. of mol.: 1 / Fragment: wrn exonuclease domain, residues 31-238 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Wrn / Plasmid: pET-28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: O09053, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides |
---|---|
#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.41 % |
---|---|
Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K |
-Data collection
Diffraction | Mean temperature: 93.15 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å |
Detector | Detector: CCD / Date: Feb 14, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 14814 / Num. obs: 14814 / % possible obs: 96 % / Redundancy: 5.2 % / Biso Wilson estimate: 7 Å2 / Rsym value: 0.092 / Net I/σ(I): 29 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 29 / Num. unique all: 14814 / Rsym value: 0.092 / % possible all: 96 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2E6L Resolution: 2→29.6 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 77755.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.3719 Å2 / ksol: 0.390643 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→29.6 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|