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Yorodumi- PDB-8ed5: Crystal structure of loop deletion AioX mutant from Pseudorhizobi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ed5 | ||||||
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Title | Crystal structure of loop deletion AioX mutant from Pseudorhizobium sp. str. NT-26 | ||||||
Components | Putative periplasmic phosphite-binding-like protein (Pbl) PtxB-like protein designated AioX | ||||||
Keywords | SIGNALING PROTEIN | ||||||
Function / homology | ABC transporter, phosphonate, periplasmic substrate-binding protein / Putative periplasmic phosphite-binding-like protein (Pbl) PtxB-like protein designated AioX Function and homology information | ||||||
Biological species | Pseudorhizobium banfieldiae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å | ||||||
Authors | Maher, M.J. / Poddar, N. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Investigating the interaction of the periplasmic arsenite-binding protein, AioX with the sensor histidine kinase, AioS from Pseudorhizobium banfieldii sp. str. NT-26 Authors: Maher, M.J. / Poddar, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ed5.cif.gz | 73.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ed5.ent.gz | 51.9 KB | Display | PDB format |
PDBx/mmJSON format | 8ed5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ed5_validation.pdf.gz | 440.8 KB | Display | wwPDB validaton report |
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Full document | 8ed5_full_validation.pdf.gz | 442.2 KB | Display | |
Data in XML | 8ed5_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 8ed5_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ed/8ed5 ftp://data.pdbj.org/pub/pdb/validation_reports/ed/8ed5 | HTTPS FTP |
-Related structure data
Related structure data | 6eskS S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 33184.387 Da / Num. of mol.: 1 / Mutation: F57A, deletion of L58-N60 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudorhizobium banfieldiae (bacteria) / Gene: aioX, NT26_p10026 / Production host: Escherichia coli (E. coli) / References: UniProt: L0NML6 | ||||
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#2: Chemical | #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: 2.78 Å3/Da / Density % sol: 55.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 25% (w/v) PEG 3350,0.2 M sodium malonate, 0.1 M Bis-Tris propane pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 1, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→47.4 Å / Num. obs: 35865 / % possible obs: 99.6 % / Redundancy: 26.4 % / CC1/2: 0.999 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 1.79→1.83 Å / Num. unique obs: 1979 / CC1/2: 0.704 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6ESK Resolution: 1.79→44.38 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.433 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.638 Å2
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Refinement step | Cycle: 1 / Resolution: 1.79→44.38 Å
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Refine LS restraints |
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