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- PDB-6qya: Crystal structure of Enteroccocus faecalis thymidylate synthase (... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6qya | ||||||||||||
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Title | Crystal structure of Enteroccocus faecalis thymidylate synthase (EfTS) in complex with dUMP | ||||||||||||
![]() | (Thymidylate synthase) x 2 | ||||||||||||
![]() | TRANSFERASE / Enteroccocus faecalis thymidylate synthase / EfTS / folate pathway / substrate / dUMP | ||||||||||||
Function / homology | ![]() thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / methylation / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Pozzi, C. / Mangani, M. | ||||||||||||
![]() | ![]() Title: Structural Comparison ofEnterococcus faecalisand Human Thymidylate Synthase Complexes with the Substrate dUMP and Its Analogue FdUMP Provides Hints about Enzyme Conformational Variabilities. Authors: Pozzi, C. / Ferrari, S. / Luciani, R. / Tassone, G. / Costi, M.P. / Mangani, S. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 530.7 KB | Display | ![]() |
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PDB format | ![]() | 437 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 64.2 KB | Display | |
Data in CIF | ![]() | 96.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6qxgC ![]() 6qxhC ![]() 6qxsC ![]() 3uwlS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 36401.977 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 36462.094 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 1478 molecules ![](data/chem/img/UMP.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/FFO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/FFO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-CL / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 2.2-2.5 M ammonium sulfate and 0.1 M HEPES, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 13, 2016 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92819 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→73.01 Å / Num. obs: 125005 / % possible obs: 95.1 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Biso Wilson estimate: 10.4 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.072 / Rrim(I) all: 0.131 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 1.76→1.86 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 18480 / CC1/2: 0.891 / Rpim(I) all: 0.233 / Rrim(I) all: 0.425 / % possible all: 96.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3UWL Resolution: 1.76→68.07 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.922 / SU B: 4.975 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.126
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.674 Å2
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Refinement step | Cycle: LAST / Resolution: 1.76→68.07 Å
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Refine LS restraints |
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