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Yorodumi- PDB-8ch2: PBP AccA from A. vitis S4 in complex with L-arabinose-2-phosphate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ch2 | ||||||
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Title | PBP AccA from A. vitis S4 in complex with L-arabinose-2-phosphate (A2P) | ||||||
Components | AccA | ||||||
Keywords | TRANSPORT PROTEIN / periplasmic binding protein / solute binding protein | ||||||
Function / homology | 2-O-phosphono-alpha-L-arabinopyranose / 2-O-phosphono-beta-L-arabinopyranose Function and homology information | ||||||
Biological species | Agrobacterium vitis S4 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.404 Å | ||||||
Authors | Morera, S. / Deicsics, G. / 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 | 8ch2.cif.gz | 300.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ch2.ent.gz | 244.6 KB | Display | PDB format |
PDBx/mmJSON format | 8ch2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ch2_validation.pdf.gz | 801.4 KB | Display | wwPDB validaton report |
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Full document | 8ch2_full_validation.pdf.gz | 804.6 KB | Display | |
Data in XML | 8ch2_validation.xml.gz | 24.4 KB | Display | |
Data in CIF | 8ch2_validation.cif.gz | 38.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ch/8ch2 ftp://data.pdbj.org/pub/pdb/validation_reports/ch/8ch2 | HTTPS FTP |
-Related structure data
Related structure data | 8c6rC 8c6uC 8c6wC 8c6yC 8c75C 8cawC 8cayC 8cb9C 8cdoC 8ch1C 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: 56652.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium vitis S4 (bacteria) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
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#2: Sugar | ChemComp-LAO / |
#3: Sugar | ChemComp-VDF / |
#4: Chemical | ChemComp-EDO / |
#5: Water | ChemComp-HOH / |
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: 2.02 Å3/Da / Density % sol: 39.24 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 8000, HEPES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.983997 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 19, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.983997 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 86791 / % possible obs: 99.8 % / Redundancy: 6.24 % / Biso Wilson estimate: 18.83 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.045 / Net I/σ(I): 30.57 |
Reflection shell | Resolution: 1.4→1.49 Å / Rmerge(I) obs: 0.881 / Num. unique obs: 13746 / CC1/2: 0.964 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.404→14.14 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.958 / SU R Cruickshank DPI: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.066 / SU Rfree Blow DPI: 0.064 / SU Rfree Cruickshank DPI: 0.061 Details: HYDROGENS WERE FULLY REFINED WITH FULL OCCUPANCY AT NUCLEAR POSITION.
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Displacement parameters | Biso mean: 26.35 Å2
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Refine analyze | Luzzati coordinate error obs: 0.15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.404→14.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.404→1.41 Å
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Refinement TLS params. | Method: refined / Origin x: 17.641 Å / Origin y: -1.3259 Å / Origin z: -19.1493 Å
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Refinement TLS group | Selection details: { A|* } |