[English] 日本語
Yorodumi- PDB-3kx7: Structural basis of the activity and substrate specificity of the... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kx7 | ||||||
---|---|---|---|---|---|---|---|
Title | Structural basis of the activity and substrate specificity of the fluoroacetyl-CoA FlK - apo wild type FlK | ||||||
Components | Fluoroacetyl-CoA thioesterase FlK | ||||||
Keywords | HYDROLASE / fluoroacetyl-CoA thioesterase FlK / thioesterase / hot-dog folding | ||||||
Function / homology | Function and homology information fluoroacetyl-CoA thioesterase / acyl-CoA hydrolase activity / protein homodimerization activity Similarity search - Function | ||||||
Biological species | Streptomyces cattleya (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å | ||||||
Authors | Dias, M.V.B. / Huang, F. / Chirgadze, D.Y. / Tosin, M. / Spiteller, D. / Valentine, E.F. / Leadlay, P.F. / Spencer, J.B. / Blundell, T.L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Structural basis for the activity and substrate specificity of fluoroacetyl-CoA thioesterase FlK. Authors: Dias, M.V. / Huang, F. / Chirgadze, D.Y. / Tosin, M. / Spiteller, D. / Dry, E.F. / Leadlay, P.F. / Spencer, J.B. / Blundell, T.L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3kx7.cif.gz | 67.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3kx7.ent.gz | 49.7 KB | Display | PDB format |
PDBx/mmJSON format | 3kx7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kx/3kx7 ftp://data.pdbj.org/pub/pdb/validation_reports/kx/3kx7 | HTTPS FTP |
---|
-Related structure data
Related structure data | 3kuvC 3kuwC 3kv7C 3kv8C 3kviC 3kvuC 3kvzC 3kw1C 3kx8C 1hnnS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
| |||||||||
Details | dimer |
-Components
#1: Protein | Mass: 15279.436 Da / Num. of mol.: 2 / Fragment: FlK Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces cattleya (bacteria) / Gene: flK, fluoroacetyl-CoA thioesterase FlK / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q1EMV2, Hydrolases #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.52 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Tris HCl 7.5 PEG 2000mme, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: 2006 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 28614 / Num. obs: 28614 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.7→1.8 Å / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Starting model: PDB entry 1HNN Resolution: 1.7→42.03 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.4 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.119 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.558 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→42.03 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.745 Å / Total num. of bins used: 20
|