[English] 日本語
![](img/lk-miru.gif)
- PDB-4js4: Crystal structure of E. coli Exonuclease I in complex with a dA16... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4js4 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of E. coli Exonuclease I in complex with a dA16 oligonucleotide | ||||||
![]() |
| ||||||
![]() | HYDROLASE/DNA / exonuclease / processive / DNA repair / DnaQ superfamily / 3'-5' ssDNA exonuclease / HYDROLASE-DNA complex | ||||||
Function / homology | ![]() exodeoxyribonuclease I / single-stranded DNA 3'-5' DNA exonuclease activity / DNA catabolic process / 5'-deoxyribose-5-phosphate lyase activity / single-stranded DNA binding / 3'-5'-RNA exonuclease activity / DNA repair / magnesium ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bell, C.E. | ||||||
![]() | ![]() Title: Crystal structures of Escherichia coli exonuclease I in complex with single-stranded DNA provide insights into the mechanism of processive digestion. Authors: Korada, S.K. / Johns, T.D. / Smith, C.E. / Jones, N.D. / McCabe, K.A. / Bell, C.E. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 204.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 160.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 464.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 468.1 KB | Display | |
Data in XML | ![]() | 32 KB | Display | |
Data in CIF | ![]() | 43.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4jrpC ![]() 4jrqC ![]() 4js5C ![]() 1fxxS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
2 | ![]()
| ||||||||||||
3 |
| ||||||||||||
Unit cell |
| ||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-
Components
#1: DNA chain | Mass: 4966.352 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemical synthesis #2: Protein | Mass: 54848.891 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-SO4 / |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.66 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 5% 2-propanol, 25% glycerol, 1.2M ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Nov 16, 2012 | |||||||||||||||
Radiation | Monochromator: Kohzu HLD-4 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
| |||||||||||||||
Reflection | Resolution: 3.1→40.6 Å / Num. all: 22917 / Num. obs: 22917 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.6 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 22.4 | |||||||||||||||
Reflection shell | Resolution: 3.1→3.27 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.813 / Mean I/σ(I) obs: 2.9 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1FXX Resolution: 3.1→40.6 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.913 / SU B: 24.025 / SU ML: 0.452 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 108.916 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→40.6 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.1→3.18 Å / Total num. of bins used: 20
|