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Open data
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Basic information
Entry | Database: PDB / ID: 1tsl | ||||||
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Title | L. CASEI THYMIDYLATE SYNTHASE WITH SPECIES SPECIFIC INHIBITOR | ||||||
![]() | THYMIDYLATE SYNTHASE | ||||||
![]() | METHYLTRANSFERASE / SPECIES SPECIFICITY / STRUCTURE-BASED DRUG DESIGN / ANTIBIOTIC | ||||||
Function / homology | ![]() thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / methylation / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Stout, T.J. / Stroud, R.M. | ||||||
![]() | ![]() Title: Structure-based design of inhibitors specific for bacterial thymidylate synthase. Authors: Stout, T.J. / Tondi, D. / Rinaldi, M. / Barlocco, D. / Pecorari, P. / Santi, D.V. / Kuntz, I.D. / Stroud, R.M. / Shoichet, B.K. / Costi, M.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 85.2 KB | Display | ![]() |
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PDB format | ![]() | 64.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 468.3 KB | Display | ![]() |
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Full document | ![]() | 475.7 KB | Display | |
Data in XML | ![]() | 8.8 KB | Display | |
Data in CIF | ![]() | 14.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1tsmC ![]() 4tmsS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36630.453 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-A15 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.11 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.8 Details: 6 MG/ML PROTEIN, PH 7.4; 1% AMMONIUM SULFATE, 1 MM DTT, + 1 % SATURATED LIGAND-DMSO SOLUTION. HANGING DROP OVER 20 MM KPO4, PH 6.8 AND 1 MM DTT., vapor diffusion - hanging drop | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Mar 1, 1994 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→48.6 Å / Num. obs: 9477 / % possible obs: 58.7 % / Observed criterion σ(I): 2 / Redundancy: 8.3 % / Biso Wilson estimate: 29.7 Å2 / Rmerge(I) obs: 0.0812 / Rsym value: 0.0812 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.5→2.75 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.125 / Mean I/σ(I) obs: 3.5 / Rsym value: 0.125 / % possible all: 24.7 |
Reflection | *PLUS Num. all: 29742 / Num. measured all: 78644 |
Reflection shell | *PLUS % possible obs: 24.7 % |
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Processing
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: PDB ENTRY 4TMS Resolution: 2.5→8 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.65 Å / Rfactor Rfree error: 0.051 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.222 |