+Open data
-Basic information
Entry | Database: PDB / ID: 8c6y | ||||||
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Title | PBP AccA from A. tumefaciens Bo542 in apoform 2 | ||||||
Components | Agrocinopine utilization periplasmic binding protein AccA | ||||||
Keywords | TRANSPORT PROTEIN / periplasmic binding protein / solute binding protein | ||||||
Function / homology | dipeptide transport / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space / Agrocinopine utilization periplasmic binding protein AccA Function and homology information | ||||||
Biological species | Agrobacterium tumefaciens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å | ||||||
Authors | Morera, S. / Vigouroux, A. / legrand, P. | ||||||
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 | 8c6y.cif.gz | 195.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8c6y.ent.gz | 157.6 KB | Display | PDB format |
PDBx/mmJSON format | 8c6y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8c6y_validation.pdf.gz | 433.6 KB | Display | wwPDB validaton report |
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Full document | 8c6y_full_validation.pdf.gz | 434 KB | Display | |
Data in XML | 8c6y_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 8c6y_validation.cif.gz | 31.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c6/8c6y ftp://data.pdbj.org/pub/pdb/validation_reports/c6/8c6y | HTTPS FTP |
-Related structure data
Related structure data | 8c6rC 8c6uC 8c6wC 8c75C 8cawC 8cayC 8cb9C 8cdoC 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
#1: Protein | Mass: 56293.750 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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#2: Chemical | ChemComp-EDO / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.75 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: PEG 4000, Na citrate, AcNH4 |
-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: Dec 10, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→49 Å / Num. obs: 40544 / % possible obs: 66.9 % / Redundancy: 14 % / CC1/2: 0.998 / Rmerge(I) obs: 0.188 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.9→1.95 Å / Rmerge(I) obs: 1.832 / Num. unique obs: 2912 / CC1/2: 0.58 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.901→22.68 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.887 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.322 / SU Rfree Blow DPI: 0.225
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Displacement parameters | Biso mean: 26.02 Å2
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Refine analyze | Luzzati coordinate error obs: 0.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.901→22.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.901→1.96 Å
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