+Open data
-Basic information
Entry | Database: PDB / ID: 8d6g | |||||||||
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Title | Nanorana parkeri saxiphilin | |||||||||
Components | Saxiphilin | |||||||||
Keywords | ANTITOXIN / Saxiphilin / Toxin resistance / Saxitoxin | |||||||||
Biological species | Nanorana parkeri (frog) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Zakrzewska, S. / Chen, Z. / Minor, D.L. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2022 Title: Definition of a saxitoxin (STX) binding code enables discovery and characterization of the anuran saxiphilin family. Authors: Chen, Z. / Zakrzewska, S. / Hajare, H.S. / Alvarez-Buylla, A. / Abderemane-Ali, F. / Bogan, M. / Ramirez, D. / O'Connell, L.A. / Du Bois, J. / Minor Jr., D.L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8d6g.cif.gz | 181.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8d6g.ent.gz | 139.4 KB | Display | PDB format |
PDBx/mmJSON format | 8d6g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d6/8d6g ftp://data.pdbj.org/pub/pdb/validation_reports/d6/8d6g | HTTPS FTP |
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-Related structure data
Related structure data | 8d6mC 8d6oC 8d6pC 8d6qC 8d6sC 8d6tC 8d6uC 6o0dS S: Starting model for refinement C: citing same article (ref.) |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 94703.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nanorana parkeri (frog) / Gene: XM_018555331.1 / Production host: Spodoptera frugiperda (fall armyworm) | ||||
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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: 3.59 Å3/Da / Density % sol: 65.78 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 20-25% v/v PEG400, 4-5% w/v PGA-LM, 100-200 mM sodium acetate, pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033167 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 2, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033167 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→43.29 Å / Num. obs: 66067 / % possible obs: 98.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 52.73 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05218 / Net I/σ(I): 12.66 |
Reflection shell | Resolution: 2.2→2.279 Å / Mean I/σ(I) obs: 0.89 / Num. unique obs: 6127 / CC1/2: 0.465 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6O0D Resolution: 2.2→43.29 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 28.62 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 152.49 Å2 / Biso mean: 66.1513 Å2 / Biso min: 30.04 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→43.29 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23
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