+Open data
-Basic information
Entry | Database: PDB / ID: 7yx1 | ||||||
---|---|---|---|---|---|---|---|
Title | Sandercyanin fluorescent protein - Y142A variant bound to BV | ||||||
Components | Sandercyanin Fluorescent Protein | ||||||
Keywords | FLUORESCENT PROTEIN / Blue fish protein / lipocalin / Biliverdin-binding protein / red-fluorescent protein | ||||||
Function / homology | Function and homology information pigment binding / response to reactive oxygen species / lipid metabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | Sander (fish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Subramanian, R. / Ghosh, S. / Yadav, K. | ||||||
Funding support | India, 1items
| ||||||
Citation | Journal: Rsc Adv / Year: 2022 Title: Modulation of biliverdin dynamics and spectral properties by Sandercyanin. Authors: Ghosh, S. / Mondal, S. / Yadav, K. / Aggarwal, S. / Schaefer, W.F. / Narayana, C. / Subramanian, R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7yx1.cif.gz | 83.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7yx1.ent.gz | 61.2 KB | Display | PDB format |
PDBx/mmJSON format | 7yx1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yx1_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7yx1_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7yx1_validation.xml.gz | 16 KB | Display | |
Data in CIF | 7yx1_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yx/7yx1 ftp://data.pdbj.org/pub/pdb/validation_reports/yx/7yx1 | HTTPS FTP |
-Related structure data
Related structure data | 7o2yC 7o3kC 5ez2S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 20067.652 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sander (fish) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1D5B367 #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: 3.86 Å3/Da / Density % sol: 68.16 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1M Bis-Tris pH 5.5 and 3M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 28, 2018 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2.65→46.57 Å / Num. obs: 18760 / % possible obs: 99.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 14.93 Å2 / CC1/2: 0.928 / Rmerge(I) obs: 0.35 / Rpim(I) all: 0.139 / Rrim(I) all: 0.378 / Net I/σ(I): 5.1 / Num. measured all: 125211 / Scaling rejects: 483 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Resolution: 2.65→2.78 Å
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5EZ2 Resolution: 2.65→46.57 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.44 / Phase error: 21.63 / 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: 100.71 Å2 / Biso mean: 20.342 Å2 / Biso min: 1.78 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.65→46.57 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7
|