[English] 日本語
![](img/lk-miru.gif)
- PDB-4r2m: Crystal Structure of R134D mutant of YnaF (Universal Stress Prote... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4r2m | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of R134D mutant of YnaF (Universal Stress Protein F) from Salmonella typhimurium | ||||||
![]() | Universal stress protein F | ||||||
![]() | UNKNOWN FUNCTION / Universal Stress Protein / HUP domain / Stress tolerance / ATP binding / Chloride binding | ||||||
Function / homology | ![]() Universal stress protein A family / UspA / Universal stress protein family / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bangera, M. / Murthy, M.R.N. | ||||||
![]() | ![]() Title: Structural and functional analysis of two universal stress proteins YdaA and YnaF from Salmonella typhimurium: possible roles in microbial stress tolerance. Authors: Bangera, M. / Panigrahi, R. / Sagurthi, S.R. / Savithri, H.S. / Murthy, M.R. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 126 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 97.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 15.2 KB | Display | |
Data in CIF | ![]() | 19.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4r2jC ![]() 4r2kC ![]() 4r2lSC C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 17300.945 Da / Num. of mol.: 2 / Mutation: R134D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: LT2 / Gene: STM1652, uspF, ynaF uspF STM1652 / Plasmid: pRSET C / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.04 % |
---|---|
Crystal grow | Temperature: 298 K / Method: under oil, microbatch / pH: 8.5 Details: 30% PEG 4000, 100mM Tris-HCl pH 8.5, 200mM Magnesium chloride, 5mM Adenosine 5'-(beta,gamma-imido)triphosphate, Under oil, Microbatch, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 20, 2014 / Details: bent collimating mirror and toroid |
Radiation | Monochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978565 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→41.48 Å / Num. obs: 15273 / % possible obs: 100 % / Redundancy: 9.7 % / Biso Wilson estimate: 32 Å2 / Rsym value: 0.12 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 9.9 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 2167 / Rsym value: 0.676 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ID 4R2L Resolution: 2.2→41.48 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.927 / SU B: 11.425 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.288 / ESU R Free: 0.209 / 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: 41.254 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→41.48 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|