[English] 日本語
![](img/lk-miru.gif)
- PDB-6xsg: Crystal structure of Staphylococcal nuclease variant Delta+PHS V6... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6xsg | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Staphylococcal nuclease variant Delta+PHS V66T at cryogenic temperature | ||||||
![]() | Thermonuclease | ||||||
![]() | HYDROLASE / nuclease / hyperstable / pdTp / polar group | ||||||
Function / homology | ![]() endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters / micrococcal nuclease / nucleic acid binding / extracellular region / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Robinson, A.C. / Schlessman, J.L. / Garcia-Moreno E., B. / Sorenson, J.L. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Crystal structure of Staphylococcal nuclease variant Delta+PHS V66T at cryogenic temperature Authors: Robinson, A.C. / Schlessman, J.L. / Garcia-Moreno E., B. / Sorenson, J.L. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 44.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 27.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 8 KB | Display | |
Data in CIF | ![]() | 10 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3bdcS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 16145.436 Da / Num. of mol.: 1 / Fragment: UNP residues 83-231 / Mutation: G50F/V51N/V66T/P117G/H124L/S128A/Del44-49 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-THP / |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.41 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 32% MPD, 25 mM potassium phosphate, calcium chloride, THP |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SEALED TUBE / Type: OTHER / Wavelength: 1.54 Å |
Detector | Type: APEX II CCD / Detector: CCD / Date: Jan 11, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 9321 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.62 % / Biso Wilson estimate: 37.3 Å2 / Rmerge(I) obs: 0.0598 / Net I/σ(I): 25.21 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 6.33 % / Rmerge(I) obs: 0.4485 / Mean I/σ(I) obs: 3.12 / Num. unique obs: 383 / % possible all: 99.5 |
-Phasing
Phasing | Method: ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Model details: Phaser MODE: MR_AUTO
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 3BDC Resolution: 2→31.84 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.219 / WRfactor Rwork: 0.1762 / FOM work R set: 0.8026 / SU B: 5.13 / SU ML: 0.137 / SU R Cruickshank DPI: 0.1994 / SU Rfree: 0.1738 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 max: 84.87 Å2 / Biso mean: 33.13 Å2 / Biso min: 17.71 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→31.84 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|