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- PDB-8cko: PBP AccA from A.tumefaciens C58 in complex with agrocinopine C-like -
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Open data
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Basic information
Entry | Database: PDB / ID: 8cko | ||||||
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Title | PBP AccA from A.tumefaciens C58 in complex with agrocinopine C-like | ||||||
![]() | ABC transporter substrate-binding protein | ||||||
![]() | TRANSPORT PROTEIN / periplasmic binding protein / solute binding protein | ||||||
Function / homology | ![]() dipeptide transport / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Morera, S. / Vigouroux, 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 | ![]() | 321.7 KB | Display | ![]() |
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PDB format | ![]() | 265.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 23 KB | Display | |
Data in CIF | ![]() | 35.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8c6rC ![]() 8c6uC ![]() 8c6wC ![]() 8c6yC ![]() 8c75C ![]() 8cawC ![]() 8cayC ![]() 8cb9C ![]() 8cdoC ![]() 8ch1C ![]() 8ch2C ![]() 8ch3C ![]() 8chcC ![]() 8ci6C ![]() 8cjuC ![]() 8ckdC ![]() 8ckeC 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 57178.102 Da / Num. of mol.: 1 / Fragment: UNP residues 30-521 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: accA Production host: ![]() ![]() References: UniProt: Q52012 | ||||||||||
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#2: Polysaccharide | Source method: isolated from a genetically manipulated source Details: Phosphodiester of D-beta-glucose (BNX) and sucrose (GLC-FRU). References: BIRD: PRD_002508 #3: Sugar | ChemComp-BNX / | ![]() Source method: isolated from a genetically manipulated source Formula: C6H13O9P Details: Phosphodiester of D-beta-glucose (BNX) and sucrose (GLC-FRU). Feature type: SUBJECT OF INVESTIGATION / References: BIRD: PRD_002508 #4: Sugar | ChemComp-ALX / | ![]() Source method: isolated from a genetically manipulated source Formula: C6H13O9P Details: Phosphodiester of D-alpha-glucose (ALX) and sucrose (GLC-FRU). Feature type: SUBJECT OF INVESTIGATION / References: BIRD: PRD_002507 #5: Water | ChemComp-HOH / | Compound details | Isomer of Agrocinopine C. Agrocinopine C is a member of the class of agrocinopines that consists of ...Isomer of Agrocinopine C. Agrocinopine C is a member of the class of agrocinopines that consists of sucrose and D-glucose joined via a phosphodiester linkage. | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.01 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: PEG 4000, NH4 acetate, citrate Na |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 7, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98011 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→78.51 Å / Num. obs: 74582 / % possible obs: 81.5 % / Redundancy: 13.5 % / Biso Wilson estimate: 20.03 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.119 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.42→1.53 Å / Rmerge(I) obs: 2.059 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3729 / CC1/2: 0.422 |
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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: 24.29 Å2
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Refine analyze | Luzzati coordinate error obs: 0.17 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.421→78.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.421→1.5 Å
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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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