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Open data
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Basic information
Entry | Database: PDB / ID: 8caw | ||||||
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Title | PBP AccA from A. tumefaciens Bo542 in complex with agrocin84 | ||||||
![]() | Agrocinopine utilization periplasmic binding protein AccA | ||||||
![]() | TRANSPORT PROTEIN / Periplasmic binding protein / solute binding protein | ||||||
Function / homology | ![]() dipeptide transport / peptide transmembrane transporter activity / peptide transport / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Morera, S. / Vigouroux, A. / El Sahili, A. | ||||||
Funding support | 1items
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![]() | ![]() Title: A highly conserved ligand-binding site for AccA transporters of antibiotic and quorum-sensing regulator in Agrobacterium leads to a different specificity. Authors: Morera, S. / Vigouroux, A. / Aumont-Nicaise, M. / Ahmar, M. / Meyer, T. / El Sahili, A. / Deicsics, G. / Gonzalez-Mula, A. / Li, S. / Dore, J. / Sirigu, S. / Legrand, P. / Penot, C. / Andre, ...Authors: Morera, S. / Vigouroux, A. / Aumont-Nicaise, M. / Ahmar, M. / Meyer, T. / El Sahili, A. / Deicsics, G. / Gonzalez-Mula, A. / Li, S. / Dore, J. / Sirigu, S. / Legrand, P. / Penot, C. / Andre, F. / Faure, D. / Soulere, L. / Queneau, Y. / Vial, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 309.7 KB | Display | ![]() |
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PDB format | ![]() | 252.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 25 KB | Display | |
Data in CIF | ![]() | 38.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8c6rC ![]() 8c6uC ![]() 8c6wC ![]() 8c6yC ![]() 8c75C ![]() 8cayC ![]() 8cb9C ![]() 8cdoC ![]() 8ch1C ![]() 8ch2C ![]() 8ch3C ![]() 8chcC ![]() 8ci6C ![]() 8cjuC ![]() 8ckdC ![]() 8ckeC ![]() 8ckoC 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: 55333.684 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: A0A2P0QK24 |
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#2: Chemical | ChemComp-C84 / [( |
#3: Chemical | ChemComp-UKU / [( |
#4: Chemical | ChemComp-EDO / |
#5: Water | ChemComp-HOH / |
Compound details | Conjugate contains beta-D-glucose (BGC) and purine (ADE). The nucleoside core, which is essential ...Conjugate contains beta-D-glucose (BGC) and purine (ADE). The nucleoside core, which is essential for toxicity, contains 3'-deoxyarabinose rather than ribose. Conjugate contains alpha-D-glucose (GLC) and purine (ADE). The nucleoside core, which is essential for toxicity, contains 3'-deoxyarabinose rather than ribose. |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.04 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG 4000, Tris-HCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 6, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 1.256→49.2 Å / Num. obs: 436693 / % possible obs: 91.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 13.85 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.256→1.27 Å / Rmerge(I) obs: 1.91 / Num. unique obs: 3461 / CC1/2: 0.157 |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS WERE FULLY REFINED WITH FULL OCCUPANCY AT NUCLEAR POSITION.
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Displacement parameters | Biso mean: 21.18 Å2
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Refine analyze | Luzzati coordinate error obs: 0.16 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.256→18.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.26→1.32 Å / Total num. of bins used: 51
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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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