[English] 日本語
Yorodumi- PDB-6ud6: Spectroscopic and structural characterization of a genetically en... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ud6 | ||||||
---|---|---|---|---|---|---|---|
Title | Spectroscopic and structural characterization of a genetically encoded direct sensor for protein-ligand interactions | ||||||
Components | Streptavidin | ||||||
Keywords | FLUORESCENT PROTEIN / unnatural amino acid / non-canonical amino acid / fluorescence / biosensor / small molecule biosensor / ligand detection | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces avidinii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.502 Å | ||||||
Authors | Mills, J.H. / Gleason, P.R. / Simmons, C.R. / Henderson, J.N. / Kartchner, B.K. | ||||||
Citation | Journal: Biochemistry / Year: 2021 Title: Structural Origins of Altered Spectroscopic Properties upon Ligand Binding in Proteins Containing a Fluorescent Noncanonical Amino Acid. Authors: Gleason, P.R. / Kolbaba-Kartchner, B. / Henderson, J.N. / Stahl, E.P. / Simmons, C.R. / Mills, J.H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6ud6.cif.gz | 71.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6ud6.ent.gz | 51.6 KB | Display | PDB format |
PDBx/mmJSON format | 6ud6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ud6_validation.pdf.gz | 458.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6ud6_full_validation.pdf.gz | 463.5 KB | Display | |
Data in XML | 6ud6_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 6ud6_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ud/6ud6 ftp://data.pdbj.org/pub/pdb/validation_reports/ud/6ud6 | HTTPS FTP |
-Related structure data
Related structure data | 6uc3C 6ud1C 6udbC 6udcC 3ry2S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
2 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 14542.706 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P22629 #2: Chemical | ChemComp-GOL / #3: Chemical | #4: 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: 2.47 Å3/Da / Density % sol: 50.21 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 3.5 Details: 500 ul of 0.1 M citric acid, pH 3.5, 3M NaCl in the reservoir with 2 ul of reservoir buffer mixed with 2 ul of 10 mg/ml of protein in the drop. Crystals were soaked to pH 5.5 overnight with 3 exchanges |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→29.631 Å / Num. obs: 44561 / % possible obs: 99.97 % / Redundancy: 13.5 % / CC1/2: 1 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.5→1.53 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2228 / CC1/2: 0.845 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3RY2 Resolution: 1.502→29.631 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.32
| ||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso max: 73.59 Å2 / Biso mean: 24.2635 Å2 / Biso min: 11.44 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.502→29.631 Å
| ||||||||||||||||||||||||
LS refinement shell | Resolution: 1.502→1.53 Å /
|