[English] 日本語
Yorodumi- PDB-1uim: Crystal Structure of Threonine Synthase from Thermus Thermophilus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uim | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Threonine Synthase from Thermus Thermophilus HB8, Orthorhombic Crystal Form | ||||||
Components | Threonine Synthase | ||||||
Keywords | LYASE / PLP-dependent enzyme / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | Function and homology information threonine synthase / threonine synthase activity / threonine biosynthetic process / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Omi, R. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: J.BIOL.CHEM. / Year: 2003 Title: Crystal Structures of Threonine Synthase from Thermus thermophilus HB8: Conformational change, substrate recognition, and mechanism. Authors: Omi, R. / Masaru, G. / Miyahara, I. / Mizuguchi, H. / Hayashi, H. / Kagamiyama, H. / Hirotsu, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1uim.cif.gz | 142.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1uim.ent.gz | 111.8 KB | Display | PDB format |
PDBx/mmJSON format | 1uim.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ui/1uim ftp://data.pdbj.org/pub/pdb/validation_reports/ui/1uim | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 37054.656 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: HB8 / Plasmid: pET20b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P83823, threonine synthase #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.52 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG8000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal grow | *PLUS Temperature: 293 K / Method: vapor diffusion, hanging drop |
Components of the solutions | *PLUS Conc.: 10 % / Common name: PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 6, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. all: 38595 / Num. obs: 38595 / % possible obs: 97.9 % |
Reflection shell | Resolution: 2.15→2.27 Å / % possible all: 97.9 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 262628 / Rmerge(I) obs: 0.105 |
Reflection shell | *PLUS % possible obs: 97.9 % / Rmerge(I) obs: 0.305 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→10 Å / σ(F): 2
| ||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→10 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.21 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.234 / Rfactor Rwork: 0.225 |