[English] 日本語
Yorodumi- PDB-4ikz: Crystal structure of peptide transporter POT (E310Q mutant) in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ikz | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of peptide transporter POT (E310Q mutant) in complex with alafosfalin | ||||||
Components | Di-tripeptide ABC transporter (Permease) | ||||||
Keywords | TRANSPORT PROTEIN / major facilitator superfamily | ||||||
Function / homology | Function and homology information oligopeptide transport / peptide transmembrane transporter activity / plasma membrane Similarity search - Function | ||||||
Biological species | Geobacillus kaustophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Doki, S. / Kato, H.E. / Ishitani, R. / Nureki, O. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Structural basis for dynamic mechanism of proton-coupled symport by the peptide transporter POT. Authors: Doki, S. / Kato, H.E. / Solcan, N. / Iwaki, M. / Koyama, M. / Hattori, M. / Iwase, N. / Tsukazaki, T. / Sugita, Y. / Kandori, H. / Newstead, S. / Ishitani, R. / Nureki, O. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4ikz.cif.gz | 104.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4ikz.ent.gz | 79.6 KB | Display | PDB format |
PDBx/mmJSON format | 4ikz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ik/4ikz ftp://data.pdbj.org/pub/pdb/validation_reports/ik/4ikz | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 54765.656 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Strain: BD53 / Gene: GK2020 / Plasmid: pCGFP-BC / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3)delta-acrB / References: UniProt: Q5KYD1*PLUS | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-AFS / | #4: Water | ChemComp-HOH / | Sequence details | AUTHORS STATE THAT THE PROTEIN WAS ISOLATED FROM STRAIN BD53 OF GEOBACILLUS SPECIES WHOSE SEQUENCE ...AUTHORS STATE THAT THE PROTEIN WAS ISOLATED FROM STRAIN BD53 OF GEOBACILLU | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.9 % / Mosaicity: 0.808 ° |
---|---|
Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 8 Details: 26% PEG 400, 100mM Tris-HCl, 300mM (NH4)2SO4, pH 8.0, lipidic cubic phase, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 3, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→50 Å / Num. obs: 18215 / % possible obs: 88.2 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.121 / Χ2: 2.18 / Net I/σ(I): 6.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→29.29 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.88 / σ(F): 1.5 / Phase error: 31.25 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.231 Å2 / ksol: 0.285 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 127.09 Å2 / Biso mean: 43.2189 Å2 / Biso min: 12.89 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→29.29 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7
|