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- PDB-4lrr: Ternary complex between E. coli thymidylate synthase, dUMP, and F9 -
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Open data
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Basic information
Entry | Database: PDB / ID: 4lrr | ||||||
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Title | Ternary complex between E. coli thymidylate synthase, dUMP, and F9 | ||||||
![]() | Thymidylate synthase | ||||||
![]() | TRANSFERASE / Thymidine monophosphate synthesis / N-terminal acetylated methionine / beta-mercaptoethanol modified cysteine | ||||||
Function / homology | ![]() thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / methylation / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mangani, S. / Pozzi, C. / Ferrari, S. / Costi, M.P. | ||||||
![]() | ![]() Title: 2'-Deoxyuridine 5'-Monophosphate Substrate Displacement in Thymidylate Synthase through 6-Hydroxy-2H-naphtho[1,8-bc]furan-2-one Derivatives. Authors: Ferrari, S. / Calo, S. / Leone, R. / Luciani, R. / Costantino, L. / Sammak, S. / Di Pisa, F. / Pozzi, C. / Mangani, 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 | ![]() | 69.3 KB | Display | ![]() |
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PDB format | ![]() | 55.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 15.5 KB | Display | |
Data in CIF | ![]() | 21.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4lrp |
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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: 30587.783 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-CF9 / | #4: Chemical | ChemComp-UMP / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3 Details: 0.1 M bicine, 3.2 M ammonium sulfate, 2 mM F9 in 10:1 v/v mixture of water/DMSO, 40 mM 2'-deoxyuridine-5'-monophosphate, pH 8.3, 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 11, 2005 |
Radiation | Monochromator: Diamond(001) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.41→65.65 Å / Num. all: 14735 / Num. obs: 14735 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Biso Wilson estimate: 26.41 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2.41→2.57 Å / Redundancy: 10 % / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2307 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 26.399 Å2
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Refine analyze | Luzzati coordinate error free: 0.233 Å | |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.41→37.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.41→2.469 Å / Total num. of bins used: 20
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