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Yorodumi- PDB-6esv: Structure of the phosphate-bound form of AioX from Rhizobium sp. ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6esv | |||||||||
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Title | Structure of the phosphate-bound form of AioX from Rhizobium sp. str. NT-26 | |||||||||
Components | Putative periplasmic phosphite-binding-like protein (Pbl) PtxB-like protein designated AioX | |||||||||
Keywords | SIGNALING PROTEIN / Periplasmic-binding protein / Arsenic / arsenite-binding / Rhizobium NT-26 | |||||||||
Function / homology | ABC transporter, phosphonate, periplasmic substrate-binding protein / PHOSPHATE ION / Putative periplasmic phosphite-binding-like protein (Pbl) PtxB-like protein designated AioX Function and homology information | |||||||||
Biological species | Rhizobium sp. NT-26 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.78 Å | |||||||||
Authors | Djordjevic, S. / Badilla, C. / Cole, A. / Santini, J. | |||||||||
Funding support | Chile, United Kingdom, 2items
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Citation | Journal: Sci Rep / Year: 2018 Title: A new family of periplasmic-binding proteins that sense arsenic oxyanions. Authors: Badilla, C. / Osborne, T.H. / Cole, A. / Watson, C. / Djordjevic, S. / Santini, J.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6esv.cif.gz | 65.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6esv.ent.gz | 50.7 KB | Display | PDB format |
PDBx/mmJSON format | 6esv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/6esv ftp://data.pdbj.org/pub/pdb/validation_reports/es/6esv | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31426.639 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: This is a Se-Met labeled protein which is why MET residues are replaced with MSE. Two residues, K230 and R173 (or K250 and R193 as numbered in the PDB file to reflect the protein numbering ...Details: This is a Se-Met labeled protein which is why MET residues are replaced with MSE. Two residues, K230 and R173 (or K250 and R193 as numbered in the PDB file to reflect the protein numbering after the transport signal peptide was removed) were modeled as Alanines due to the disorder for the side chain. Similarly, residues 37 and 38 (57 and 58) were not modeled due to disorder. Source: (gene. exp.) Rhizobium sp. NT-26 (bacteria) / Gene: aioX, NT26_p10026 / Production host: Escherichia coli (E. coli) / References: UniProt: L0NML6 |
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#2: Chemical | ChemComp-PO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.85 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 0.49 M NaH2PO4 and 0.91 M K2HPO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.978 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 13, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→88.07 Å / Num. obs: 36718 / % possible obs: 99.8 % / Redundancy: 16.4 % / Net I/σ(I): 19.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.78→88.07 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.67 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.103 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.742 Å2
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Refinement step | Cycle: 1 / Resolution: 1.78→88.07 Å
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Refine LS restraints |
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