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Open data
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Basic information
Entry | Database: PDB / ID: 6ghj | |||||||||
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Title | PepTSt in complex with tripeptide Phe-Ala-Gln | |||||||||
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![]() | MEMBRANE PROTEIN / MFS / POT / peptide transporter | |||||||||
Function / homology | ![]() oligopeptide transport / peptide transmembrane transporter activity / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Martinez Molledo, M. / Quistgaard, E.M. / Loew, C. | |||||||||
Funding support | 2items
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![]() | ![]() Title: Tripeptide binding in a proton-dependent oligopeptide transporter. Authors: Martinez Molledo, M. / Quistgaard, E.M. / 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 | ![]() | 114.3 KB | Display | ![]() |
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PDB format | ![]() | 87.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 22.7 KB | Display | |
Data in CIF | ![]() | 30.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5oxoS S: Starting model for refinement |
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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 / Protein/peptide , 2 types, 2 molecules AB
#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: ![]() ![]() |
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#2: Protein/peptide | Mass: 364.396 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) |
-Non-polymers , 7 types, 121 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/78N.gif)
![](data/chem/img/78M.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/78N.gif)
![](data/chem/img/78M.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-1PE / | #5: Chemical | ChemComp-EPE / | #6: Chemical | ChemComp-NA / | #7: Chemical | ChemComp-78N / ( #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.36 % |
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Crystal grow | Temperature: 292.15 K / Method: lipidic cubic phase Details: 0.1-0.3 M HEPES buffer pH 7.5, 250 mM ammonium phosphate monobasic (NH4H2PO4), PEG400 (15-25%) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 7, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9143 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→48.69 Å / Num. obs: 29604 / % possible obs: 99.73 % / Redundancy: 10.3 % / Biso Wilson estimate: 40.59 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Net I/σ(I): 19.44 |
Reflection shell | Resolution: 2.26→2.341 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 3.19 / CC1/2: 0.871 / % possible all: 99.79 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5OXO Resolution: 2.26→48.69 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.69
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.26→48.69 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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