+Open data
-Basic information
Entry | Database: PDB / ID: 8d6m | |||||||||
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Title | Nanorana parkeri saxiphilin:STX (co-crystal) | |||||||||
Components | Saxiphilin | |||||||||
Keywords | ANTITOXIN / Saxiphilin / Toxin resistance / Saxitoxin | |||||||||
Function / homology | Chem-9SL Function and homology information | |||||||||
Biological species | Nanorana parkeri (frog) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 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 | 8d6m.cif.gz | 184.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8d6m.ent.gz | 140.9 KB | Display | PDB format |
PDBx/mmJSON format | 8d6m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d6/8d6m ftp://data.pdbj.org/pub/pdb/validation_reports/d6/8d6m | HTTPS FTP |
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-Related structure data
Related structure data | 8d6gSC 8d6oC 8d6pC 8d6qC 8d6sC 8d6tC 8d6uC S: Starting model for refinement 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: 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 | ChemComp-1PE / |
#3: Chemical | ChemComp-9SL / [( |
#4: 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: 3.58 Å3/Da / Density % sol: 65.62 % |
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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, STX:NpSxph molar ratio 1.2:1 |
-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 22, 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→42.55 Å / Num. obs: 88641 / % possible obs: 99.89 % / Redundancy: 5.2 % / Biso Wilson estimate: 49.89 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.05456 / Net I/σ(I): 14.11 |
Reflection shell | Resolution: 2→2.071 Å / Mean I/σ(I) obs: 1.11 / Num. unique obs: 8856 / CC1/2: 0.637 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 8D6G Resolution: 2→42.55 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 27.31 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→42.55 Å
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Refine LS restraints |
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LS refinement shell |
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