+
Open data
-
Basic information
Entry | Database: PDB / ID: 5d6k | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | PepT - CIM | |||||||||
![]() | Di-or tripeptide:H+ symporter | |||||||||
![]() | TRANSPORT PROTEIN / ALPHA-HELICAL / Major Facilitator Superfamily (MFS) Transporters / PepTSt Oligopeptide-proton symporter (POT family) | |||||||||
Function / homology | ![]() oligopeptide transport / peptide transmembrane transporter activity / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ma, P. / Caffrey, M. | |||||||||
Funding support | ![]() ![]()
| |||||||||
![]() | ![]() Title: The cubicon method for concentrating membrane proteins in the cubic mesophase. Authors: Ma, P. / Weichert, D. / Aleksandrov, L.A. / Jensen, T.J. / Riordan, J.R. / Liu, X. / Kobilka, B.K. / Caffrey, M. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 105.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 81 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 19 KB | Display | |
Data in CIF | ![]() | 25.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5d6iC ![]() 5d6lC ![]() 5iyuC ![]() 4d2bS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 52782.148 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC BAA-250 / LMG 18311 / Gene: dtpT, stu0970 / Production host: ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-PO4 / | ||||
#3: Chemical | ChemComp-97M / ( #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.04 % |
---|---|
Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 17-22.5 %(V/V) PEG 400, 0.1 M HEPES PH 7.0 AND 0.15-0.48 M NH4H2PO4. CRYSTALS WERE GROWN BY THE LCP METHOD USING 9.7 MAG AS HOSTING LIPID. PH range: 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50.85 Å / Num. obs: 25142 / % possible obs: 99.8 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.4→2.46 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.964 / Mean I/σ(I) obs: 1.8 / % possible all: 99.4 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4D2B Resolution: 2.4→50.845 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.2 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→50.845 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|