[English] 日本語
![](img/lk-miru.gif)
- PDB-4xgb: Crystal Structure of E112A/H234A Mutant of Stationary Phase Survi... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4xgb | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of E112A/H234A Mutant of Stationary Phase Survival Protein (SurE) from Salmonella typhimurium co-crystallized with AMP | ||||||
![]() | 5'/3'-nucleotidase SurE | ||||||
![]() | HYDROLASE / Stationary phase survival protein / Domain swapping / Rossmann fold like / Phosphatase | ||||||
Function / homology | ![]() 3'-nucleotidase / exopolyphosphatase / 3'-nucleotidase activity / exopolyphosphatase activity / XMP 5'-nucleosidase activity / 5'-nucleotidase / 5'-nucleotidase activity / nucleotide binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Mathiharan, Y.K. / Murthy, M.R.N. | ||||||
![]() | ![]() Title: Insights into stabilizing interactions in the distorted domain-swapped dimer of Salmonella typhimurium survival protein. Authors: Mathiharan, Y.K. / Savithri, H.S. / Murthy, M.R. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 223 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 176.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 477 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 484.8 KB | Display | |
Data in XML | ![]() | 46.3 KB | Display | |
Data in CIF | ![]() | 67.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4rytC ![]() 4ryuC ![]() 4xepC ![]() 4xerSC ![]() 4xgpC ![]() 4xh8C ![]() 4xj7C C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 28490.008 Da / Num. of mol.: 4 / Mutation: E112A, H234A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P66881, 5'-nucleotidase, 3'-nucleotidase, exopolyphosphatase #2: Chemical | ChemComp-MG / #3: Chemical | #4: Chemical | ChemComp-MPD / ( | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.4 % |
---|---|
Crystal grow | Temperature: 293 K / Method: microbatch / pH: 4.6 Details: 0.02M Calcium chloride, 0.1 M sodium acetate (pH 4.6) and 30 % 2 methyl 2,4 pentanediol |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 7, 2013 |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→59.38 Å / Num. obs: 67404 / % possible obs: 94.6 % / Redundancy: 2.6 % / Biso Wilson estimate: 15 Å2 / Rsym value: 0.133 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 2.21→2.33 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 2.6 / % possible all: 75.6 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4XER Resolution: 2.23→59.38 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.87 / SU B: 7.565 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 25.23 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.23→59.38 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|