[English] 日本語
![](img/lk-miru.gif)
- PDB-3l9u: Crystal Structure of Salmonella enterica serovar Typhimurium DsbL -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3l9u | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Salmonella enterica serovar Typhimurium DsbL | ||||||
![]() | Disulfide isomerase | ||||||
![]() | OXIDOREDUCTASE / thioredoxin-fold / DsbL / thiol-disulfide oxidoreductase / Isomerase | ||||||
Function / homology | ![]() protein-disulfide reductase activity / isomerase activity / periplasmic space Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Heras, B. / Jarrott, R. / Shouldice, S.R. / Guncar, G. | ||||||
![]() | ![]() Title: Structural and functional characterization of three DsbA paralogues from Salmonella enterica serovar typhimurium Authors: Heras, B. / Totsika, M. / Jarrott, R. / Shouldice, S.R. / Guncar, G. / Achard, M.E.S. / Wells, T.J. / Argente, M.P. / McEwan, A.G. / Schembri, M.A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 99.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 74.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 409.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 410.4 KB | Display | |
Data in XML | ![]() | 12.4 KB | Display | |
Data in CIF | ![]() | 18.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3l9sC ![]() 3l9vC ![]() 3c7mS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||
Unit cell |
| |||||||||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 22226.443 Da / Num. of mol.: 1 / Fragment: UNP residues 25-223 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: SL1344 / Gene: dsbL, STM3193 / Plasmid: pETLIC / Production host: ![]() ![]() References: UniProt: E1WHY0, UniProt: Q8ZLZ0*PLUS, protein disulfide-isomerase |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.46 % / Mosaicity: 0.418 ° |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 2.6-3.4 M sodium malonate pH 7.0 -7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 15, 2008 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.956667 Å / Relative weight: 1 |
Reflection | Resolution: 1.568→50 Å / Num. all: 34491 / Num. obs: 34491 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.066 / Χ2: 1.056 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.57→1.6 Å / Redundancy: 7 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 4.12 / Num. unique all: 1693 / Χ2: 0.92 / % possible all: 100 |
-Phasing
Phasing | Method: ![]() |
---|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3C7M Resolution: 1.568→28.404 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.903 / SU ML: 0.13 / σ(F): 1.35 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.469 Å2 / ksol: 0.413 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 58.83 Å2 / Biso mean: 19.668 Å2 / Biso min: 7.95 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.568→28.404 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
|