[English] 日本語
![](img/lk-miru.gif)
- PDB-5fbd: S1 nuclease from Aspergillus oryzae in complex with phosphate and... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5fbd | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | S1 nuclease from Aspergillus oryzae in complex with phosphate and 2'-deoxycytidine | ||||||||||||
![]() | Nuclease S1 | ||||||||||||
![]() | HYDROLASE / Endonuclease / Zinc dependent / Complex | ||||||||||||
Function / homology | ![]() Aspergillus nuclease S1 / nuclease activity / DNA catabolic process / endonuclease activity / nucleic acid binding / metal ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() | ||||||||||||
![]() | Koval, T. / Oestergaard, L.H. / Dohnalek, J. | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() Title: Structural and Catalytic Properties of S1 Nuclease from Aspergillus oryzae Responsible for Substrate Recognition, Cleavage, Non-Specificity, and Inhibition. Authors: Koval, T. / stergaard, L.H. / Lehmbeck, J. / Nrgaard, A. / Lipovova, P. / Duskova, J. / Skalova, T. / Trundova, M. / Kolenko, P. / Fejfarova, K. / Stransky, J. / Svecova, L. / Hasek, J. / Dohnalek, J. | ||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 79.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 55.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 457.6 KB | Display | |
Data in XML | ![]() | 15.7 KB | Display | |
Data in CIF | ![]() | 24.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5fb9C ![]() 5fbaC ![]() 5fbbC ![]() 5fbcC ![]() 5fbfC ![]() 5fbgC C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein / Sugars , 2 types, 2 molecules A![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: Protein | Mass: 29083.660 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Mature protein without signal sequence. / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#3: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 382 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/DCZ.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/DCZ.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #4: Chemical | ChemComp-PO4 / | #5: Chemical | ChemComp-DCZ / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.9 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 3.8 Details: 0.1 M Citric acid pH 3.8, 25% w/v Polyethylene glycol 3,350 Temp details: stable |
-Data collection
Diffraction | Mean temperature: 120 K |
---|---|
Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54056 Å |
Detector | Type: AGILENT ATLAS CCD / Detector: CCD / Date: Oct 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54056 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→30.08 Å / Num. obs: 22221 / % possible obs: 95.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 5.1 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 2.1 / % possible all: 72.2 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: our previous model of S1 Resolution: 1.75→30.08 Å / Cor.coef. Fo:Fc: 0.963 / SU B: 2.212 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.124 / 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: 11.744 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.75→30.08 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|