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- PDB-5m4z: Crystal structure of the complex of T.spiralis thymidylate syntha... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5m4z | ||||||
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Title | Crystal structure of the complex of T.spiralis thymidylate synthase with N(4)-hydroxy-2'-deoxycytidine-5'-monophosphate, crystallized in the presence of N(5,10)-methylenetetrahydrofolate | ||||||
![]() | Thymidylate synthase | ||||||
![]() | TRANSFERASE / enzyme-inhibitor complex / high-resolution structure / anticancer target | ||||||
Function / homology | ![]() thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / methylation Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wilk, P. / Maj, P. / Jarmula, A. / Dowiercial, A. / Rode, W. | ||||||
![]() | ![]() Title: Molecular Mechanism of Thymidylate Synthase Inhibition by N 4 -Hydroxy-dCMP in View of Spectrophotometric and Crystallographic Studies. Authors: Maj, P. / Jarmula, A. / Wilk, P. / Prokopowicz, M. / Rypniewski, W. / Zielinski, Z. / Dowiercial, A. / Bzowska, A. / Rode, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 358.7 KB | Display | ![]() |
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PDB format | ![]() | 299 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 24.6 KB | Display | |
Data in CIF | ![]() | 35.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6f6zC ![]() 4g9u 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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Unit cell |
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Components
#1: Protein | Mass: 37240.371 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.46 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.1 / Details: 0.1M NaF pH 7.1, 19% PEG 3350, 0.02% NaN3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 1.179→28.092 Å / Num. obs: 172936 / % possible obs: 97.41 % / Redundancy: 3.61 % / CC1/2: 1 / Rmerge(I) obs: 0.034 / Rsym value: 0.04 / Net I/σ(I): 16.43 |
Reflection shell | Resolution: 1.179→1.21 Å / % possible all: 89 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4g9u ![]() 4g9u Resolution: 1.179→28.092 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 17.22
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 130.28 Å2 / Biso mean: 23.8067 Å2 / Biso min: 8.17 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.179→28.092 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13
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