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- PDB-8qlh: Crystal structure of the pneumococcal Substrate-binding protein A... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8qlh | ||||||
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Title | Crystal structure of the pneumococcal Substrate-binding protein AliC as a domain-swapped dimer | ||||||
![]() | AliC | ||||||
![]() | PEPTIDE BINDING PROTEIN / Permease / Pneumococcus / AliC / peptide / substrate-binding protein | ||||||
Function / homology | ![]() peptide transport / ATP-binding cassette (ABC) transporter complex / transmembrane transport / protein transport / periplasmic space Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Alcorlo, M. / Abdullah, M.R. / Hammerschmidt, S. / Hermoso, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular and structural basis of oligopeptide recognition by the Ami transporter system in pneumococci. Authors: Alcorlo, M. / Abdullah, M.R. / Steil, L. / Sotomayor, F. / Lopez-de Oro, L. / de Castro, S. / Velazquez, S. / Kohler, T.P. / Jimenez, E. / Medina, A. / Uson, I. / Keller, L.E. / Bradshaw, J. ...Authors: Alcorlo, M. / Abdullah, M.R. / Steil, L. / Sotomayor, F. / Lopez-de Oro, L. / de Castro, S. / Velazquez, S. / Kohler, T.P. / Jimenez, E. / Medina, A. / Uson, I. / Keller, L.E. / Bradshaw, J.L. / McDaniel, L.S. / Camarasa, M.J. / Volker, U. / Hammerschmidt, S. / Hermoso, J.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 262 KB | Display | ![]() |
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PDB format | ![]() | 209 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 415.7 KB | Display | ![]() |
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Full document | ![]() | 419.1 KB | Display | |
Data in XML | ![]() | 23.2 KB | Display | |
Data in CIF | ![]() | 32.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8a42C ![]() 8qlcC ![]() 8qlgC ![]() 8qljC ![]() 8qlkC ![]() 8qlmC ![]() 8qlvC ![]() 8qm0C 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
#1: Protein | Mass: 70460.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.42 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris pH=6.5 and 25% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 13, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→57.52 Å / Num. obs: 28215 / % possible obs: 98.9 % / Redundancy: 5.2 % / CC1/2: 0.99 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.38→2.46 Å / Rmerge(I) obs: 0.657 / Num. unique obs: 2820 / CC1/2: 0.8 |
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Processing
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Refinement | Method to determine structure: ![]()
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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 max: 126.2 Å2 / Biso mean: 58.4017 Å2 / Biso min: 29.08 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.38→57.519 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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