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Open data
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Basic information
Entry | Database: PDB / ID: 4xni | |||||||||
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Title | X-ray structure of PepTst1 | |||||||||
![]() | Di-or tripeptide:H+ symporter | |||||||||
![]() | TRANSPORT PROTEIN / peptide transporter | |||||||||
Function / homology | ![]() oligopeptide transport / peptide transmembrane transporter activity / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Huang, C.Y. / Olieric, V. / Diederichs, K. / Wang, M. / Caffrey, M. | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: In meso in situ serial X-ray crystallography of soluble and membrane proteins. Authors: Huang, C.Y. / Olieric, V. / Ma, P. / Panepucci, E. / Diederichs, K. / Wang, M. / Caffrey, M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102.9 KB | Display | ![]() |
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PDB format | ![]() | 80.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 19.7 KB | Display | |
Data in CIF | ![]() | 26.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4xjbC ![]() 4xjdC ![]() 4xjfC ![]() 4xjgC ![]() 4xjhC ![]() 4xjiC ![]() 4xnjC ![]() 4xnkC ![]() 4xnlC ![]() 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
#1: Protein | Mass: 52782.148 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: dtpT, stu0970 / Production host: ![]() ![]() | ||||
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#2: Chemical | ChemComp-78M / ( #3: Chemical | ChemComp-PO4 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.7 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 250-350 mM NH4H2PO4, 100 mM HEPES, pH7.0, 21-22% pEG400 |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 3, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 17128 / % possible obs: 99.9 % / Redundancy: 10.1 % / Net I/σ(I): 4 |
Reflection shell | Resolution: 2.8→2.87 Å / Redundancy: 9.8 % / Mean I/σ(I) obs: 1.1 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4D2B Resolution: 2.8→48.161 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.72 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→48.161 Å
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Refine LS restraints |
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LS refinement shell |
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