[English] 日本語
Yorodumi- PDB-2yye: Crystal structure of selenophosphate synthetase from Aquifex aeol... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yye | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of selenophosphate synthetase from Aquifex aeolicus complexed with AMPCPP | ||||||
Components | Selenide, water dikinase | ||||||
Keywords | TRANSFERASE / Full-length selenophosphate synthetase complex with ATP-analog / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information selenide, water dikinase / selenide, water dikinase activity / selenocysteine biosynthetic process / phosphorylation / magnesium ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Itoh, Y. / Sekine, S. / Matsumoto, E. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Structure of selenophosphate synthetase essential for selenium incorporation into proteins and RNAs Authors: Itoh, Y. / Sekine, S. / Matsumoto, E. / Akasaka, R. / Takemoto, C. / Shirouzu, M. / Yokoyama, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2yye.cif.gz | 153 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2yye.ent.gz | 118.8 KB | Display | PDB format |
PDBx/mmJSON format | 2yye.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yy/2yye ftp://data.pdbj.org/pub/pdb/validation_reports/yy/2yye | HTTPS FTP |
---|
-Related structure data
Related structure data | 2zodC 2yyd 2e0b C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 37697.309 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: aq_1030 / Plasmid: pCold TF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O67139, selenide, water dikinase #2: Chemical | ChemComp-CO / #3: Chemical | #4: Chemical | ChemComp-PO4 / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.32 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.4 Details: 17% PEG8000, 50mM KH2PO4, 0.1M MES, 1mM AMPCPP, 5mM CoCl2, pH 6.4, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 27, 2006 / Details: monochromater |
Radiation | Monochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 36487 / % possible obs: 99.9 % / Redundancy: 6 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.108 / Rsym value: 0.108 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 6 % / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 3 / Num. unique all: 3592 / Rsym value: 0.682 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2YYD 2yyd Resolution: 2.1→42.47 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2374350.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: We replaced selenocysteine 13 by Cys to facilitate the protein expression
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.2407 Å2 / ksol: 0.367882 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.7 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→42.47 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|