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- PDB-6ei9: Crystal structure of E. coli tRNA-dihydrouridine synthase B (DusB) -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ei9 | ||||||
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Title | Crystal structure of E. coli tRNA-dihydrouridine synthase B (DusB) | ||||||
![]() | tRNA-dihydrouridine synthase B | ||||||
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Function / homology | ![]() tRNA dihydrouridine synthase activity / ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bou-Nader, C. / Hamdane, D. | ||||||
![]() | ![]() Title: Unveiling structural and functional divergences of bacterial tRNA dihydrouridine synthases: perspectives on the evolution scenario. Authors: Bou-Nader, C. / Montemont, H. / Guerineau, V. / Jean-Jean, O. / Bregeon, D. / Hamdane, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 268.4 KB | Display | ![]() |
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PDB format | ![]() | 215.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4bfaS 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 , 1 types, 2 molecules AB
#1: Protein | Mass: 37945.305 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: P0ABT7, UniProt: P0ABT5*PLUS, ![]() |
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-Non-polymers , 5 types, 153 molecules ![](data/chem/img/FMN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ![]() #3: Chemical | ![]() #4: Chemical | ChemComp-SO4 / ![]() #5: Chemical | ChemComp-EPE / | ![]() #6: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.99 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.6 M lithium sulfate 100 mM HEPES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 26, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.55→48.51 Å / Num. obs: 26834 / % possible obs: 99.94 % / Redundancy: 7.8 % / Biso Wilson estimate: 94.27 Å2 / CC1/2: 1 / Rsym value: 0.05516 / Net I/σ(I): 18.96 |
Reflection shell | Resolution: 2.55→2.641 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 0.84 / Num. unique obs: 2675 / CC1/2: 0.43 / Rsym value: 1.753 / % possible all: 100 |
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Processing
Software |
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Refinement | Method to determine structure![]() ![]() Starting model: 4BFA Resolution: 2.55→48.51 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.418 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.404 / SU Rfree Blow DPI: 0.253 / SU Rfree Cruickshank DPI: 0.258
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Displacement parameters | Biso mean: 92.35 Å2
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Refine analyze | Luzzati coordinate error obs: 0.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.55→48.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.65 Å / Rfactor Rfree error: 0 / Total num. of bins used: 13
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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