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Yorodumi- PDB-6udb: Spectroscopic and structural characterization of a genetically en... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6udb | ||||||
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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: 1.55 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6udb.cif.gz | 120.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6udb.ent.gz | 91.4 KB | Display | PDB format |
PDBx/mmJSON format | 6udb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6udb_validation.pdf.gz | 471.4 KB | Display | wwPDB validaton report |
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Full document | 6udb_full_validation.pdf.gz | 477.1 KB | Display | |
Data in XML | 6udb_validation.xml.gz | 26.3 KB | Display | |
Data in CIF | 6udb_validation.cif.gz | 37.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ud/6udb ftp://data.pdbj.org/pub/pdb/validation_reports/ud/6udb | HTTPS FTP |
-Related structure data
Related structure data | 6uc3C 6ud1C 6ud6C 6udcC 3ry2S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14615.757 Da / Num. of mol.: 4 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-PEG / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.51 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 500 ul of 0.1 M Bis-Tris, pH 6.5, 25% w/v polyethylene glycol 3350 in the reservoir with 2 ul of reservoir buffer mixed with 2 ul of 10 mg/ml of protein in the drop |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 18, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→42.78 Å / Num. obs: 64849 / % possible obs: 99.6 % / Redundancy: 1 % / CC1/2: 0.923 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.55→1.58 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3014 / CC1/2: 0.938 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3RY2 Resolution: 1.55→42.78 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.046 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.082 / Details: U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 82.22 Å2 / Biso mean: 28.433 Å2 / Biso min: 13.61 Å2
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Refinement step | Cycle: final / Resolution: 1.55→42.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Rfactor Rfree error: 0
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