+Open data
-Basic information
Entry | Database: PDB / ID: 4xni | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | X-ray structure of PepTst1 | |||||||||
Components | Di-or tripeptide:H+ symporter | |||||||||
Keywords | TRANSPORT PROTEIN / peptide transporter | |||||||||
Function / homology | Function and homology information oligopeptide transport / peptide transmembrane transporter activity / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Streptococcus thermophilus LMG 18311 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Huang, C.Y. / Olieric, V. / Diederichs, K. / Wang, M. / Caffrey, M. | |||||||||
Funding support | Ireland, United States, 2items
| |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4xni.cif.gz | 102.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4xni.ent.gz | 80.1 KB | Display | PDB format |
PDBx/mmJSON format | 4xni.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xn/4xni ftp://data.pdbj.org/pub/pdb/validation_reports/xn/4xni | 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 (ref.) |
---|---|
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.) Streptococcus thermophilus LMG 18311 (bacteria) Gene: dtpT, stu0970 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5M4H8 | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-78M / ( #3: Chemical | ChemComp-PO4 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.7 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.033 Å |
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 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| |||||||||||||||||||||||||||||||||||||||||||||||||
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
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|