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Open data
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Basic information
Entry | Database: PDB / ID: 5oxp | ||||||
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Title | PepTSt in occluded conformation with phosphate ion bound | ||||||
![]() | 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 204.1 KB | Display | ![]() |
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PDB format | ![]() | 165.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5oxkC ![]() 5oxlC ![]() 5oxmC ![]() 5oxnC ![]() 5oxoC ![]() 5oxqC ![]() 6eiaC ![]() 4d2bS 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 , 5 types, 60 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/78N.gif)
![](data/chem/img/78M.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/78N.gif)
![](data/chem/img/78M.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PO4 / ![]() #3: Chemical | ![]() #4: Chemical | ChemComp-78N / ( #5: Chemical | #6: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.26 % |
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Crystal grow![]() | Temperature: 292.15 K / Method: lipidic cubic phase Details: 0.1 M sodium phosphate pH 6.5, 0.25 M ammonium phosphate monobasic, 24% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.372→49.04 Å / Num. obs: 24769 / % possible obs: 99.58 % / Redundancy: 6.5 % / Biso Wilson estimate: 58.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09354 / Net I/σ(I): 14.09 |
Reflection shell | Resolution: 2.372→2.457 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1.17 / Num. unique obs: 2386 / CC1/2: 0.477 / % possible all: 97.27 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4D2B Resolution: 2.372→49.037 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.02
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.372→49.037 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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