+
Open data
-
Basic information
Entry | Database: PDB / ID: 1a0t | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | SUCROSE-SPECIFIC PORIN, WITH BOUND SUCROSE MOLECULES | |||||||||
![]() | SUCROSE-SPECIFIC PORIN | |||||||||
![]() | OUTER MEMBRANE PROTEIN / PORIN | |||||||||
Function / homology | ![]() polysaccharide transport / porin activity / pore complex / carbohydrate transmembrane transporter activity / monoatomic ion transport / cell outer membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Diederichs, K. / Welte, W. | |||||||||
![]() | ![]() Title: Structure of the sucrose-specific porin ScrY from Salmonella typhimurium and its complex with sucrose. Authors: Forst, D. / Welte, W. / Wacker, T. / Diederichs, K. #1: ![]() Title: Crystallization and Preliminary X-Ray Diffraction Analysis of Scry, a Specific Bacterial Outer Membrane Porin Authors: Forst, D. / Schulein, K. / Wacker, T. / Diederichs, K. / Kreutz, W. / Benz, R. / Welte, W. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 254.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 204.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.7 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 2.7 MB | Display | |
Data in XML | ![]() | 50 KB | Display | |
Data in CIF | ![]() | 69.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1a0sC ![]() 1aosS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS oper:
|
-
Components
#1: Protein | Mass: 45333.668 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Polysaccharide | beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 68 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Method: vapor diffusion, sitting drop / pH: 7.7 Details: PROTEIN WAS CRYSTALLIZED BY VAPOR DIFFUSION USING THE SITTING-DROP METHOD. THE DROP CONTAINED 5-7 MG/ML PROTEIN, 20 MM TRIS/CL AT PH 7.7, 100MM LICL, 20MM MGSO4, 1.2% BETA-D- ...Details: PROTEIN WAS CRYSTALLIZED BY VAPOR DIFFUSION USING THE SITTING-DROP METHOD. THE DROP CONTAINED 5-7 MG/ML PROTEIN, 20 MM TRIS/CL AT PH 7.7, 100MM LICL, 20MM MGSO4, 1.2% BETA-D-OCTYLGLUCOPYRANOSIDE AND 6-9% PEG-2000. THE CONCENTRATION OF PEG IN THE RESERVOIR WAS 12-15%. 2M SUCROSE WAS ADDED TO THE DROP FOR COCRYSTALLIZATION., vapor diffusion - sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 287 K |
---|---|
Diffraction source | Type: OTHER / Wavelength: 1.5418 |
Detector | Type: STOE / Detector: DIFFRACTOMETER / Date: Apr 1, 1995 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→17 Å / Num. obs: 65815 / % possible obs: 80.7 % / Observed criterion σ(I): 0 / Redundancy: 2.74 % / Biso Wilson estimate: 19.4 Å2 / Rsym value: 0.155 / Net I/σ(I): 5 |
Reflection shell | Resolution: 2.4→3 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2 / Rsym value: 0.524 / % possible all: 84 |
Reflection | *PLUS Rmerge(I) obs: 0.161 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: SUCROSE PORIN (PDB ENTRY 1AOS) Resolution: 2.4→100 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→100 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Rms dev position: 0.1 Å / Weight Biso : 1 / Weight position: 50
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.49 Å / Rfactor Rfree error: 0.058 / Total num. of bins used: 10
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|