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Yorodumi- PDB-8cdo: PBP AccA-F144YG440Q from A. tumefaciens Bo542 in complex with agr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8cdo | ||||||
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Title | PBP AccA-F144YG440Q from A. tumefaciens Bo542 in complex with agrocinopine C-like | ||||||
Components | Agrocinopine utilization periplasmic binding protein AccA | ||||||
Keywords | TRANSPORT PROTEIN / periplasmic binding protein / solute binding protein | ||||||
Function / homology | Function and homology information ATP-binding cassette (ABC) transporter complex / transmembrane transport / outer membrane-bounded periplasmic space Similarity search - Function | ||||||
Biological species | Agrobacterium tumefaciens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å | ||||||
Authors | Morera, S. / Vigouroux, A. | ||||||
Funding support | 1items
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Citation | Journal: Biochem.J. / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cdo.cif.gz | 312 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cdo.ent.gz | 254.6 KB | Display | PDB format |
PDBx/mmJSON format | 8cdo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cdo_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 8cdo_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8cdo_validation.xml.gz | 25.4 KB | Display | |
Data in CIF | 8cdo_validation.cif.gz | 40.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cd/8cdo ftp://data.pdbj.org/pub/pdb/validation_reports/cd/8cdo | HTTPS FTP |
-Related structure data
Related structure data | 8c6rC 8c6uC 8c6wC 8c6yC 8c75C 8cawC 8cayC 8cb9C 8ch1C 8ch2C 8ch3C 8chcC 8ci6C 8cjuC 8ckdC 8ckeC 8ckoC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 56380.828 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: Bo542 / Gene: accA, AgrTiChry5_232 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A2P0QK24 |
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-Sugars , 3 types, 4 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source Details: Phosphodiester of D-beta-glucose (BNX) and sucrose (GLC-FRU). References: BIRD: PRD_002548 #7: Sugar | ChemComp-BNX / | Type: D-saccharide, beta linking, Oligosaccharide / Class: Nutrient / Mass: 260.136 Da / Num. of mol.: 1 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_002548 #8: Sugar | ChemComp-ALX / | |
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-Non-polymers , 5 types, 628 molecules
#3: Chemical | ChemComp-PG4 / | ||||
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#4: Chemical | ChemComp-PEG / | ||||
#5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-PGE / | #9: Water | ChemComp-HOH / | |
-Details
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. |
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Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.36 % |
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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: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 12, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.32→86.3 Å / Num. obs: 135341 / % possible obs: 95.6 % / Redundancy: 40.9 % / Biso Wilson estimate: 19.27 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.102 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 1.32→1.36 Å / Rmerge(I) obs: 3.27 / Num. unique obs: 6758 / CC1/2: 0.635 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.32→19.31 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.97 / SU R Cruickshank DPI: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.042 / SU Rfree Blow DPI: 0.044 / SU Rfree Cruickshank DPI: 0.042 Details: HYDROGENS WERE FULLY REFINED WITH FULL OCCUPANCY AT NUCLEAR POSITION.
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Displacement parameters | Biso mean: 22.14 Å2
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Refine analyze | Luzzati coordinate error obs: 0.13 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.32→19.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.32→1.34 Å / Total num. of bins used: 51
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Refinement TLS params. | Method: refined / Origin x: 8.9353 Å / Origin y: 29.0439 Å / Origin z: -6.8148 Å
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Refinement TLS group | Selection details: { A|* } |