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Open data
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Basic information
Entry | Database: PDB / ID: 4kar | ||||||
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Title | Crystal structure of FDTS (TM0449) mutant (H53D) with FAD | ||||||
![]() | Thymidylate synthase | ||||||
![]() | TRANSFERASE / thyX / FDTS / H53D mutant / FAD / Novel FDTS fold / Convertion of dUMP to dTMP using Tetrahydrofolate / and NAD(P)H | ||||||
Function / homology | ![]() thymidylate synthase (FAD) / thymidylate synthase (FAD) activity / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / NADPH binding / flavin adenine dinucleotide binding / methylation Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mathews, I.I. | ||||||
![]() | ![]() Title: Flavin-Dependent Thymidylate Synthase as a Drug Target for Deadly Microbes: Mutational Study and a Strategy for Inhibitor Design. Authors: Mathews, I.I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 195.5 KB | Display | ![]() |
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PDB format | ![]() | 156.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 34.7 KB | Display | |
Data in CIF | ![]() | 46.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4kasC ![]() 4katC ![]() 1o26S C: citing same article ( S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 27480.621 Da / Num. of mol.: 4 / Fragment: TM0449 (unp residues 1-220) / Mutation: H53D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-2PE / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.26 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 50 - 60% PEG200, 0.1Tris.HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 23, 2004 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→38.2 Å / Num. all: 58450 / Num. obs: 58450 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 2.03→2.08 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.881 / Mean I/σ(I) obs: 1.87 / Num. unique all: 4269 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1O26 Resolution: 2.03→38.15 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.859 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.22 / ESU R Free: 0.189 / 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: 44.451 Å2
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Refinement step | Cycle: LAST / Resolution: 2.03→38.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.03→2.083 Å / Total num. of bins used: 20
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