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Open data
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Basic information
Entry | Database: PDB / ID: 4d2b | ||||||
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Title | Structure of a ligand free POT family peptide transporter | ||||||
![]() | DI-OR TRIPEPTIDE\:H+ SYMPORTER | ||||||
![]() | TRANSPORT PROTEIN / MAJOR FACILITATOR SUPERFAMILY / PROTON OLIGOPEPTIDE TRANSPORTER (POT) FAMILY / PEPTIDE TRANSPORTER | ||||||
Function / homology | ![]() oligopeptide transport / peptide transmembrane transporter activity / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lyons, J.A. / Parker, J.L. / Solcan, N. / Brinth, A. / Li, D. / Shah, S.T.A. / Caffrey, M. / Newstead, S. | ||||||
![]() | ![]() Title: Structural Basis for Polyspecificity in the Pot Family of Proton-Coupled Oligopeptide Transporters. Authors: Lyons, J.A. / Parker, J.L. / Solcan, N. / Brinth, A. / Li, D. / Shah, S.T. / Caffrey, M. / Newstead, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 104.1 KB | Display | ![]() |
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PDB format | ![]() | 80.3 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 | ![]() | 19.5 KB | Display | |
Data in CIF | ![]() | 26.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4d2cC ![]() 4d2dC ![]() 4apsS C: citing same article ( 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
#1: Protein | Mass: 53721.125 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | ChemComp-78N / ( #3: Chemical | ChemComp-78M / ( #4: Chemical | ChemComp-PO4 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.66 % / Description: NONE |
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Crystal grow | Method: lipidic cubic phase / pH: 7 Details: 16-23 %(V/V) PEG 400, 0.1 M HEPES PH 7.0 AND 0.15-0.55 M NH4H2PO4. CRYSTALS WERE GROWN BY THE LCP METHOD USING 7.8 MAG AS HOSTING LIPID. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 14, 2012 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→39.1 Å / Num. obs: 26241 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 46.95 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.35→2.48 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.2 / % possible all: 98 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4APS Resolution: 2.35→39.099 Å / SU ML: 0.25 / σ(F): 1.35 / Phase error: 24.89 / Stereochemistry target values: ML Details: RESIDUES 1-5, 346-348, 413-422, 473-491 ARE DISORDERED
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.268 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→39.099 Å
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Refine LS restraints |
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LS refinement shell |
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