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- PDB-3bnz: Crystal structure of Thymidylate Synthase ternary complex with dU... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3bnz | ||||||
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Title | Crystal structure of Thymidylate Synthase ternary complex with dUMP and 8A inhibitor | ||||||
![]() | Thymidylate synthase | ||||||
![]() | TRANSFERASE / Thymidylate Synthase / Methyltransferase / Nucleotide biosynthesis | ||||||
Function / homology | ![]() thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / methylation / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Leone, R. / Cancian, L. / Luciani, R. / Ferrari, S. / Costi, M.P. / Mangani, S. | ||||||
![]() | ![]() Title: Identification of the binding modes of N-phenylphthalimides inhibiting bacterial thymidylate synthase through X-ray crystallography screening Authors: Mangani, S. / Cancian, L. / Leone, R. / Pozzi, C. / Lazzari, S. / Luciani, R. / Ferrari, S. / 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 | ![]() | 79.2 KB | Display | ![]() |
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PDB format | ![]() | 58.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 942.3 KB | Display | ![]() |
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Full document | ![]() | 961.8 KB | Display | |
Data in XML | ![]() | 17.3 KB | Display | |
Data in CIF | ![]() | 23.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3byxC ![]() 3bz0C ![]() 3c06C ![]() 3c0aC ![]() 3ijzC ![]() 3ik0C ![]() 3ik1C ![]() 1lcaS 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 on special symmetry positions |
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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-UMP / |
#4: Chemical | ChemComp-C16 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 100mM (NH4)H2PO4/(NH4)2HPO4, 5% v/v PEG 400, 20mM Tris-HCl buffer pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 15, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→48.468 Å / Num. all: 12116 / Num. obs: 11978 / Biso Wilson estimate: 59.33 Å2 / Rmerge(I) obs: 0.169 / Rsym value: 0.169 |
Reflection shell | Resolution: 2.6→2.74 Å / Rmerge(I) obs: 0.418 / Num. unique all: 1715 / Rsym value: 0.418 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1LCA Resolution: 2.6→36.04 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.833 / Cross valid method: THROUGHOUT / ESU R: 1.305 / ESU R Free: 0.418 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.236 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→36.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.668 Å / Total num. of bins used: 20
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