+Open data
-Basic information
Entry | Database: PDB / ID: 8d6s | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Rana catesbeiana saxiphilin mutant - Y558A:STX (co-crystal) | |||||||||
Components | Saxiphilin | |||||||||
Keywords | ANTITOXIN / Saxiphilin / Toxin resistance / Saxitoxin | |||||||||
Function / homology | Function and homology information recycling endosome / iron ion transport / antibacterial humoral response / early endosome / extracellular space / plasma membrane Similarity search - Function | |||||||||
Biological species | Lithobates catesbeianus (American bullfrog) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | |||||||||
Authors | Chen, Z. / Zakrzewska, S. / Minor, D.L. | |||||||||
Funding support | United States, 2items
| |||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8d6s.cif.gz | 653.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8d6s.ent.gz | 540.4 KB | Display | PDB format |
PDBx/mmJSON format | 8d6s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8d6s_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8d6s_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8d6s_validation.xml.gz | 57.3 KB | Display | |
Data in CIF | 8d6s_validation.cif.gz | 76.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d6/8d6s ftp://data.pdbj.org/pub/pdb/validation_reports/d6/8d6s | HTTPS FTP |
-Related structure data
Related structure data | 8d6gC 8d6mC 8d6oC 8d6pC 8d6qC 8d6tC 8d6uC 6o0fS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 93860.914 Da / Num. of mol.: 2 / Mutation: Y558A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lithobates catesbeianus (American bullfrog) Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P31226 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.47 Å3/Da / Density % sol: 64.5 % |
---|---|
Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop Details: 0.08-0.2 M sodium cacodylate, pH 6.5, 5% PEG8000, 33% MPD, STX:Saxiphilin molar ratio 1.1:1 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033167 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 26, 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: 2.6→47.37 Å / Num. obs: 81054 / % possible obs: 99.9 % / Redundancy: 13.4 % / Biso Wilson estimate: 84.83 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.115 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.6→2.65 Å / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4377 / CC1/2: 0.458 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6O0F Resolution: 2.6→47.37 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 38.84 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 272.4 Å2 / Biso mean: 135.8571 Å2 / Biso min: 62.67 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.6→47.37 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -1.2523 Å / Origin y: 28.22 Å / Origin z: -32.0551 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|