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Yorodumi- PDB-1c3q: CRYSTAL STRUCTURE OF NATIVE THIAZOLE KINASE IN THE MONOCLINIC FORM -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c3q | ||||||
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Title | CRYSTAL STRUCTURE OF NATIVE THIAZOLE KINASE IN THE MONOCLINIC FORM | ||||||
Components | Hydroxyethylthiazole kinase | ||||||
Keywords | TRANSFERASE / ALPHA-BETA / ATP BINDING / KINASE | ||||||
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: 2 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 | 1c3q.cif.gz | 164.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c3q.ent.gz | 131 KB | Display | PDB format |
PDBx/mmJSON format | 1c3q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/1c3q ftp://data.pdbj.org/pub/pdb/validation_reports/c3/1c3q | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29645.695 Da / Num. of mol.: 3 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: Chemical | ChemComp-CL / | #3: Chemical | #4: 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: 2.24 Å3/Da / Density % sol: 45.07 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.6 / Details: 100 MM TRIS, 20 % (W/V) PEG 8000, pH 8.60 | ||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 44 % | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, sitting dropDetails: drop consists of equal volume of protein and reservoir solutions | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.922 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 7, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.922 Å / Relative weight: 1 |
Reflection | Resolution: 2→36.5 Å / Num. obs: 220523 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.275 / % possible all: 85.4 |
Reflection | *PLUS Num. obs: 51102 / Num. measured all: 162565 |
Reflection shell | *PLUS % possible obs: 95 % / Mean I/σ(I) obs: 5.8 |
-Processing
Software |
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Refinement | Resolution: 2→20 Å / σ(F): 1 / Stereochemistry target values: ENGH & HUBER Details: USED TORSION ANGLE, SIMULATED ANNEALING WITH MAXIMUM LIKELIHOOD TARGET.
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: 'CNS' / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.251 / Rfactor Rwork: 0.218 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.269 / Rfactor Rwork: 0.28 |