[English] 日本語
Yorodumi- PDB-1tmk: YEAST THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE MONOPHOSPHATE (DTMP) -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tmk | ||||||
---|---|---|---|---|---|---|---|
Title | YEAST THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE MONOPHOSPHATE (DTMP) | ||||||
Components | THYMIDYLATE KINASE | ||||||
Keywords | PHOSPHOTRANSFERASE / TRANSFERASE (PHOSPHOTRANSFERASE) / KINASE / THYMIDINE ACTIVATION PATHWAY / ENZYME | ||||||
Function / homology | Function and homology information UMP/dUMP kinase activity / dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / nucleoside diphosphate kinase activity / dTTP biosynthetic process / phosphorylation / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SIR WITH NCS / Resolution: 2.1 Å | ||||||
Authors | Lavie, A. / Schlichting, I. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1997 Title: Structure of thymidylate kinase reveals the cause behind the limiting step in AZT activation. Authors: Lavie, A. / Vetter, I.R. / Konrad, M. / Goody, R.S. / Reinstein, J. / Schlichting, I. #1: Journal: Nat.Med. (N.Y.) / Year: 1997 Title: The Bottleneck in Azt Activation Authors: Lavie, A. / Schlichting, I. / Vetter, I.R. / Konrad, M. / Reinstein, J. / Goody, R.S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1tmk.cif.gz | 100.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1tmk.ent.gz | 76.5 KB | Display | PDB format |
PDBx/mmJSON format | 1tmk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tm/1tmk ftp://data.pdbj.org/pub/pdb/validation_reports/tm/1tmk | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.9838, -0.1627, -0.0758), Vector: |
-Components
#1: Protein | Mass: 24719.375 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: CDC8 / Production host: Escherichia coli (E. coli) / References: UniProt: P00572, dTMP kinase #2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 51 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7.5 / Details: 30% PEG 4000 100 MM HEPES PH 7.5 25 MM MGAC | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Apr 1, 1996 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→12.67 Å / Num. obs: 25398 / % possible obs: 88.5 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rsym value: 0.065 |
Reflection shell | Resolution: 2.1→2.14 Å / Rsym value: 0.281 / % possible all: 65.4 |
Reflection | *PLUS Num. measured all: 51803 / Rmerge(I) obs: 0.065 |
Reflection shell | *PLUS % possible obs: 65.4 % / Rmerge(I) obs: 0.281 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SIR WITH NCS / Resolution: 2.1→10 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.14 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor obs: 0.2589 |