[English] 日本語
Yorodumi- PDB-4w6v: Crystal structure of a peptide transporter from Yersinia enteroco... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4w6v | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a peptide transporter from Yersinia enterocolitica at 3 A resolution | ||||||
Components | Di-/tripeptide transporter | ||||||
Keywords | TRANSPORT PROTEIN / membrane protein / solute transporter / permease | ||||||
Function / homology | Function and homology information oligopeptide transport / peptide transmembrane transporter activity / protein transport / membrane => GO:0016020 / plasma membrane Similarity search - Function | ||||||
Biological species | Yersinia enterocolitica subsp. palearctica YE-P4 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.01819 Å | ||||||
Authors | Jeckelmann, J.-M. / Boggavarapu, R. / Harder, D. / Ucurum, Z. / Fotiadis, D. | ||||||
Funding support | Switzerland, 1items
| ||||||
Citation | Journal: Bmc Biol. / Year: 2015 Title: Role of electrostatic interactions for ligand recognition and specificity of peptide transporters. Authors: Boggavarapu, R. / Jeckelmann, J.M. / Harder, D. / Ucurum, Z. / Fotiadis, D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4w6v.cif.gz | 104.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4w6v.ent.gz | 79.8 KB | Display | PDB format |
PDBx/mmJSON format | 4w6v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w6/4w6v ftp://data.pdbj.org/pub/pdb/validation_reports/w6/4w6v | HTTPS FTP |
---|
-Related structure data
Related structure data | 4ikvS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | biological unit is the same as asym. |
-Components
#1: Protein | Mass: 56509.898 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Two missing loops Source: (gene. exp.) Yersinia enterocolitica subsp. palearctica YE-P4 (bacteria) Gene: YEP4_02370 / Plasmid: pET21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: R9G739, UniProt: A0A2R9TD79*PLUS |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.09 Å3/Da / Density % sol: 69.9 % / Description: orthorhombic |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.4 / Details: PEG 300, NaCl, Li2SO4, LiH2PO4 / PH range: 4.0 - 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 25, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.01819→46.2977 Å / Num. obs: 19398 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 104.04 Å2 / Net I/σ(I): 20 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
|
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR |
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4IKV Resolution: 3.01819→46.2977 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / Phase error: 33.14 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 277.8 Å2 / Biso mean: 105.7227 Å2 / Biso min: 46.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.01819→46.2977 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13
|