[English] 日本語
Yorodumi- PDB-1jg0: Crystal structure of Escherichia coli thymidylate synthase comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jg0 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Escherichia coli thymidylate synthase complexed with 2'-deoxyuridine-5'-monophosphate and N,O-didansyl-L-tyrosine | ||||||
Components | thymidylate synthase | ||||||
Keywords | TRANSFERASE / thymidylate synthase / didansyl tyrosine | ||||||
Function / homology | Function and homology information thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / response to radiation / regulation of translation / methylation / magnesium ion binding / protein homodimerization activity / RNA binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Fritz, T.A. / Tondi, D. / Finer-Moore, J.S. / Costi, M.P. / Stroud, R.M. | ||||||
Citation | Journal: Chem.Biol. / Year: 2001 Title: Predicting and harnessing protein flexibility in the design of species-specific inhibitors of thymidylate synthase. Authors: Fritz, T.A. / Tondi, D. / Finer-Moore, J.S. / Costi, M.P. / Stroud, R.M. #1: Journal: Chem.Biol. / Year: 1999 Title: Structure-based discovery and in- parallel optimization of novel competitive inhibitors of thymidylate synthase | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1jg0.cif.gz | 126.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1jg0.ent.gz | 104.9 KB | Display | PDB format |
PDBx/mmJSON format | 1jg0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jg0_validation.pdf.gz | 601.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1jg0_full_validation.pdf.gz | 617.4 KB | Display | |
Data in XML | 1jg0_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 1jg0_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/1jg0 ftp://data.pdbj.org/pub/pdb/validation_reports/jg/1jg0 | HTTPS FTP |
-Related structure data
Related structure data | 1synS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 30387.432 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: Esherichia coli / Production host: Escherichia coli (E. coli) / Strain (production host): X2913 / References: UniProt: P0A884, thymidylate synthase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.89 % | ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 18-20% PEG 4000, 0.2 M sodium acetate, 0.1 M Tris, 5 mM dithiothreitol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 26, 1999 |
Radiation | Monochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2→27.42 Å / Num. all: 41243 / Num. obs: 41069 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 4.06 / Num. unique all: 4040 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 333240 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SYN WITH WATER AND LIGANDS REMOVED FROM THE MODEL Resolution: 2→27.42 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2140489.74 / Data cutoff high rms absF: 2140489.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| |||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.03 Å2 / ksol: 0.332 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.7 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→27.42 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
| |||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 3.7 % / Rfactor obs: 0.212 / Rfactor Rfree: 0.25 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 28.6 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
| |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.321 / % reflection Rfree: 3.6 % / Rfactor Rwork: 0.282 |