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Open data
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Basic information
Entry | Database: PDB / ID: 5oxk | |||||||||
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Title | PepTSt in complex with dipeptide Ala-Gln | |||||||||
![]() | Di-or tripeptide:H+ symporter | |||||||||
![]() | TRANSPORT PROTEIN / alpha helical membrane protein / MFS fold / membrane protein / peptide transporter | |||||||||
Function / homology | ![]() oligopeptide transport / peptide transmembrane transporter activity / identical protein binding / plasma membrane 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 193 KB | Display | ![]() |
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PDB format | ![]() | 154.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 20.8 KB | Display | |
Data in CIF | ![]() | 27.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5oxlC ![]() 5oxmC ![]() 5oxnC ![]() 5oxoC ![]() 5oxpC ![]() 5oxqC ![]() 6eiaC ![]() 4d2cS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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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.) ![]() Strain: ATCC BAA-250 / LMG 18311 / Gene: dtpT, stu0970 / Production host: ![]() ![]() |
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-Non-polymers , 7 types, 66 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/78N.gif)
![](data/chem/img/78M.gif)
![](data/chem/img/ALA.gif)
![](data/chem/img/GLN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/78N.gif)
![](data/chem/img/78M.gif)
![](data/chem/img/ALA.gif)
![](data/chem/img/GLN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-1PE / | #4: Chemical | ChemComp-78N / ( #5: Chemical | ChemComp-78M / ( | #6: Chemical | ChemComp-ALA / | #7: Chemical | ChemComp-GLN / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.6 % |
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Crystal grow | Temperature: 292.15 K / Method: lipidic cubic phase Details: 0.1 M HEPES pH 7.0, 0.15-0.55 M ammonium phosphate monobasic, 16-23% PEG 400 100 mM Ala-Gln added to the mesophase |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 20, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→48.81 Å / Num. obs: 23772 / % possible obs: 99.74 % / Redundancy: 13.2 % / Biso Wilson estimate: 47.07 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.107 / Net I/σ(I): 18.75 |
Reflection shell | Resolution: 2.38→2.465 Å / Mean I/σ(I) obs: 2.56 / Num. unique obs: 2330 / CC1/2: 0.832 / % possible all: 99.91 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4D2C Resolution: 2.38→48.81 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.13
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.38→48.81 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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