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Yorodumi- PDB-1ekq: CRYSTAL STRUCTURE OF HYDROXYETHYLTHIAZOLE KINASE IN R3 SPACE GROUP -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ekq | ||||||
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Title | CRYSTAL STRUCTURE OF HYDROXYETHYLTHIAZOLE KINASE IN R3 SPACE GROUP | ||||||
Components | HYDROXYETHYLTHIAZOLE KINASE | ||||||
Keywords | TRANSFERASE / Alpha-beta | ||||||
Function / homology | Function and homology information hydroxyethylthiazole kinase / hydroxyethylthiazole kinase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / phosphorylation / magnesium ion binding / ATP binding Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å | ||||||
Authors | Campobasso, N. / Mathews, I.I. / Begley, T.P. / Ealick, S.E. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Crystal structure of 4-methyl-5-beta-hydroxyethylthiazole kinase from Bacillus subtilis at 1.5 A resolution. Authors: Campobasso, N. / Mathews, I.I. / Begley, T.P. / Ealick, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ekq.cif.gz | 103.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ekq.ent.gz | 84.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ekq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/1ekq ftp://data.pdbj.org/pub/pdb/validation_reports/ek/1ekq | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Details | Biological assembly is a trimer. The crystallographic three-fold generates two trimers from chain A and chain B, respectively. |
-Components
#1: Protein | Mass: 28272.166 Da / Num. of mol.: 2 / Mutation: C198(CSD) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P39593, hydroxyethylthiazole kinase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.76 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100mM Tris, 100mM ammonium sulfate, 30% PEG4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 49 % | |||||||||||||||||||||||||
Crystal grow | *PLUS Details: drop consists of equal volume of protein and reservoir solutions | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.914 |
Detector | Type: ADSC QUANTUM 1 / Detector: CCD / Date: Apr 14, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.914 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→20 Å / Num. all: 83000 / Num. obs: 73978 / % possible obs: 89 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.5→1.57 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.158 / % possible all: 55 |
Reflection | *PLUS Num. measured all: 264643 |
Reflection shell | *PLUS % possible obs: 55 % / Mean I/σ(I) obs: 4 |
-Processing
Software |
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Refinement | Resolution: 1.5→20 Å / σ(F): 2 / σ(I): 1 / Stereochemistry target values: engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.5→20 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 1.57 Å / Rfactor Rfree: 0.306 / Rfactor Rwork: 0.291 |