[English] 日本語
Yorodumi- PDB-3nl2: The Crystal Structure of Candida glabrata THI6, a Bifunctional En... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nl2 | ||||||
---|---|---|---|---|---|---|---|
Title | The Crystal Structure of Candida glabrata THI6, a Bifunctional Enzyme involved in Thiamin Biosyhthesis of Eukaryotes | ||||||
Components | Thiamine biosynthetic bifunctional enzyme | ||||||
Keywords | TRANSFERASE / THI6 / Bifunctional Enzyme / Thiamin Biosynthesis / Eukaryoyes | ||||||
Function / homology | Function and homology information hydroxyethylthiazole kinase activity / thiamine-phosphate diphosphorylase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / magnesium ion binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Candida glabrata (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.08 Å | ||||||
Authors | Paul, D. / Chatterjee, A. / Begley, T.P. / Ealick, S.E. | ||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Domain Organization in Candida glabrata THI6, a Bifunctional Enzyme Required for Thiamin Biosynthesis in Eukaryotes . Authors: Paul, D. / Chatterjee, A. / Begley, T.P. / Ealick, S.E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3nl2.cif.gz | 547.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3nl2.ent.gz | 453.4 KB | Display | PDB format |
PDBx/mmJSON format | 3nl2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nl/3nl2 ftp://data.pdbj.org/pub/pdb/validation_reports/nl/3nl2 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
|
-Components
#1: Protein | Mass: 58126.605 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida glabrata (fungus) / Gene: CAGL0E05808g, THI6 / Plasmid: THT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Star(DE3) References: UniProt: Q6FV03, thiamine phosphate synthase, hydroxyethylthiazole kinase |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.22 Å3/Da / Density % sol: 61.84 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 30% PEG400, 200 mM MgCl2, 100 mM HEPES, pH 7.5, vapor diffusion, hanging drop, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 21, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 3.08→37 Å / Num. all: 75076 / Num. obs: 75076 |
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.08→37 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 2.94 / σ(F): 0.06 / Phase error: 25.74 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.976 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.08→37 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|