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Open data
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Basic information
Entry | Database: PDB / ID: 8b1i | ||||||
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Title | DtpB-Nb132-MS | ||||||
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![]() | MEMBRANE PROTEIN / MFS / Proton coupled Oligopeptide Transporter | ||||||
Function / homology | ![]() tripeptide transmembrane transport / dipeptide transmembrane transport / tripeptide transmembrane transporter activity / peptide:proton symporter activity / dipeptide transmembrane transporter activity / peptide transport / proton transmembrane transporter activity / proton transmembrane transport / protein transport / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Killer, M. / Finocchio, G. / Lei, J. / Jungnickel, K. / Kotov, V. / Steinke, J. / Bartels, K. / Strauss, J. / Dupeux, F. / Humm, A.S. ...Killer, M. / Finocchio, G. / Lei, J. / Jungnickel, K. / Kotov, V. / Steinke, J. / Bartels, K. / Strauss, J. / Dupeux, F. / Humm, A.S. / Cornaciu, I. / Marquez, J. / Pardon, E. / Steyeart, J. / Loew, C. | ||||||
Funding support | 1items
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![]() | ![]() Title: Plasticity of the binding pocket in peptide transporters underpins promiscuous substrate recognition. Authors: Kotov, V. / Killer, M. / Jungnickel, K.E.J. / Lei, J. / Finocchio, G. / Steinke, J. / Bartels, K. / Strauss, J. / Dupeux, F. / Humm, A.S. / Cornaciu, I. / Marquez, J.A. / Pardon, E. / Steyaert, J. / Low, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 140.7 KB | Display | ![]() |
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PDB format | ![]() | 102.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8b17C ![]() 8b18C ![]() 8b19C ![]() 8b1aC ![]() 8b1bC ![]() 8b1cC ![]() 8b1dC ![]() 8b1eC ![]() 8b1fC ![]() 8b1gC ![]() 8b1hC ![]() 8b1jC ![]() 8b1kC ![]() 6gs4S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein / Antibody / Protein/peptide / Sugars , 4 types, 4 molecules ABC![](data/chem/img/LMT.gif)
![](data/chem/img/LMT.gif)
#1: Protein | Mass: 53607.746 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Antibody | Mass: 13788.445 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein/peptide | Mass: 236.289 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
#4: Sugar | ChemComp-LMT / |
-Non-polymers , 8 types, 141 molecules ![](data/chem/img/OCT.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/D12.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/D10.gif)
![](data/chem/img/HEX.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/D12.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/D10.gif)
![](data/chem/img/HEX.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-OCT / | ||||||||||||
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#6: Chemical | ChemComp-PG4 / #7: Chemical | #8: Chemical | ChemComp-D12 / | #9: Chemical | #10: Chemical | ChemComp-D10 / | #11: Chemical | #12: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.18 Å3/Da / Density % sol: 70.59 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion Details: 100 mM MES pH 6.0, 30-40 % PEG 400 100-300 mM NaCl, 200 mM BaCl2, and 20 mM MS |
-Data collection
Diffraction | Mean temperature: 292 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 11, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→50.95 Å / Num. obs: 71403 / % possible obs: 99.92 % / Redundancy: 2 % / Biso Wilson estimate: 54.22 Å2 / CC1/2: 1 / Net I/σ(I): 9.44 |
Reflection shell | Resolution: 2.55→2.641 Å / Num. unique obs: 3707 / CC1/2: 0.545 |
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Processing
Software | Name: PHENIX / Version: 1.19.2_4158 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: 6GS4 Resolution: 2.55→50.95 Å / SU ML: 0.4004 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.1909 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 61.75 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→50.95 Å
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Refine LS restraints |
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LS refinement shell |
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