[English] 日本語
![](img/lk-miru.gif)
- PDB-4f3s: Crystal structure of periplasmic D-alanine ABC transporter from S... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4f3s | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of periplasmic D-alanine ABC transporter from Salmonella enterica | |||||||||
![]() | Putative periplasmic binding protein | |||||||||
![]() | TRANSPORT PROTEIN / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / periplasmic | |||||||||
Function / homology | ![]() Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Agarwal, R. / Chamala, S. / Evans, B. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Siedel, R. / Villigas, G. / Zencheck, W. ...Agarwal, R. / Chamala, S. / Evans, B. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Siedel, R. / Villigas, G. / Zencheck, W. / Foti, R. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC) | |||||||||
![]() | ![]() Title: Crystal structure of periplasmic D-alanine ABC transporter from Salmonella enterica Authors: Agarwal, R. / Almo, S.C. / Swaminathan, S. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 56.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 44.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Similar structure data | |
---|---|
Other databases |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 29598.467 Da / Num. of mol.: 1 / Fragment: UNP residues 23-253 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: STM1633 / Plasmid: pET / Production host: ![]() ![]() |
---|---|
#2: Chemical | ChemComp-GLY / |
#3: Chemical | ChemComp-DAL / |
#4: Chemical | ChemComp-PO4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.28 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.8M Ammonium citrate tribasic pH 7, 10% Jeffamine M600 pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 22, 2011 / Details: Mirrors |
Radiation | Monochromator: SI-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→50 Å / Num. all: 20516 / Num. obs: 20516 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 41 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.14→2.22 Å / Redundancy: 37.83 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 5 / Num. unique all: 2004 / % possible all: 97.3 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.385 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.14→46.45 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.141→2.197 Å / Total num. of bins used: 20
|