+
Open data
-
Basic information
Entry | Database: PDB / ID: 6eia | ||||||
---|---|---|---|---|---|---|---|
Title | PepTSt in complex with HEPES (100 mM) | ||||||
![]() | Di-or tripeptide:H+ symporter | ||||||
![]() | ![]() | ||||||
Function / homology | ![]() oligopeptide transport / peptide transmembrane transporter activity / identical protein binding / ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Martinez Molledo, M. / Quistgaard, E.M. / Loew, C. | ||||||
![]() | ![]() Title: Multispecific Substrate Recognition in a Proton-Dependent Oligopeptide Transporter. Authors: Martinez Molledo, M. / Quistgaard, E.M. / Flayhan, A. / Pieprzyk, J. / Low, C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 207.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 166.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 5oxkC ![]() 5oxlC ![]() 5oxmC ![]() 5oxnC ![]() 5oxoC ![]() 5oxpC ![]() 5oxqC ![]() 4d2dS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 53648.074 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
---|
-Non-polymers , 6 types, 147 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/78N.gif)
![](data/chem/img/78M.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/78N.gif)
![](data/chem/img/78M.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PO4 / ![]() #3: Chemical | ChemComp-PG4 / | ![]() #4: Chemical | ![]() #5: Chemical | ChemComp-78N / ( #6: Chemical | ChemComp-78M / ( #7: Water | ChemComp-HOH / | ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.66 % |
---|---|
Crystal grow![]() | Temperature: 292.15 K / Method: lipidic cubic phase Details: 0.1 M HEPES pH 7.0, 0.23M ammonium phosphate monobasic, 19% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2→49.25 Å / Num. all: 556226 / Num. obs: 42456 / % possible obs: 99.8 % / Redundancy: 13.1 % / Biso Wilson estimate: 41.15 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0651 / Net I/σ(I): 23.25 |
Reflection shell | Resolution: 2→2.072 Å / Redundancy: 13.2 % / Mean I/σ(I) obs: 2.33 / Num. unique all: 55100 / Num. unique obs: 4167 / CC1/2: 0.766 / % possible all: 99.52 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: 4D2D Resolution: 2→49.25 Å / SU ML: 0.2 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 19.63
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→49.25 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|