+Open data
-Basic information
Entry | Database: PDB / ID: 4it6 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of amino acid residues 1-120 of CG17282 | ||||||
Components | CG17282 | ||||||
Keywords | UNKNOWN FUNCTION / FK506-binding protein / Ubiquitous | ||||||
Function / homology | Function and homology information regulation of post-translational protein modification / regulation of establishment of planar polarity / kinase activator activity / regulation of protein catabolic process / regulation of intracellular protein transport / locomotor rhythm / cytosol Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å | ||||||
Authors | Bouyain, S. / Agyekum, B. / Hall, D.R. | ||||||
Citation | Journal: Neuron / Year: 2013 Title: Noncanonical FK506-Binding Protein BDBT Binds DBT to Enhance Its Circadian Function and Forms Foci at Night. Authors: Fan, J.Y. / Agyekum, B. / Venkatesan, A. / Hall, D.R. / Keightley, A. / Bjes, E.S. / Bouyain, S. / Price, J.L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4it6.cif.gz | 57.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4it6.ent.gz | 45.1 KB | Display | PDB format |
PDBx/mmJSON format | 4it6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4it6_validation.pdf.gz | 463.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4it6_full_validation.pdf.gz | 468.6 KB | Display | |
Data in XML | 4it6_validation.xml.gz | 13 KB | Display | |
Data in CIF | 4it6_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/it/4it6 ftp://data.pdbj.org/pub/pdb/validation_reports/it/4it6 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 13935.392 Da / Num. of mol.: 2 / Fragment: UNP Residues 1-120 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG17282, Dmel_CG17282 / Plasmid: pT7HMP / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q9VDE4 #2: Chemical | ChemComp-FMT / #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.34 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: 4M sodium formate pH 6.9, 0.1 M Na-cacodylate pH 6.5 and 1% (w/v) polyethylene glycol 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97243, 0.97934 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 7, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 6.4 % / Av σ(I) over netI: 13.98 / Number: 130707 / Rmerge(I) obs: 0.117 / Χ2: 0.97 / D res high: 1.9 Å / D res low: 50 Å / Num. obs: 20305 / % possible obs: 95.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→50 Å / Num. obs: 20495 / % possible obs: 96.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.114 / Χ2: 0.997 / Net I/σ(I): 7.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 1.9→30.412 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.775 / SU ML: 0.66 / σ(F): 2 / Phase error: 29.38 / Stereochemistry target values: MLHL
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.733 Å2 / ksol: 0.376 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 64.54 Å2 / Biso mean: 30.7034 Å2 / Biso min: 18.8 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→30.412 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
|