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- PDB-6scy: U34-tRNA thiolase NcsA from Methanococcus maripaludis with its [4... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6scy | ||||||
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Title | U34-tRNA thiolase NcsA from Methanococcus maripaludis with its [4Fe-4S] cluster | ||||||
![]() | ([4Fe-4S]-dependent U34-ARNt ...) x 2 | ||||||
![]() | RNA BINDING PROTEIN / tRNA thiolase / iron-sulfur cluster | ||||||
Function / homology | ![]() tRNA thio-modification / tRNA wobble uridine modification / transferase activity / tRNA binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bimai, O. / Legrand, P. / Golinelli-Pimpaneau, B. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The thiolation of uridine 34 in tRNA, which controls protein translation, depends on a [4Fe-4S] cluster in the archaeum Methanococcus maripaludis. Authors: Bimai, O. / Legrand, P. / Ravanat, J.L. / Touati, N. / Zhou, J. / He, N. / Lenon, M. / Barras, F. / Fontecave, M. / Golinelli-Pimpaneau, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 276.3 KB | Display | ![]() |
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PDB format | ![]() | 225.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3vrhS 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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Unit cell |
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Components
-[4Fe-4S]-dependent U34-ARNt ... , 2 types, 2 molecules AB
#1: Protein | [ Mass: 35127.176 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: MMP1356 / Production host: ![]() ![]() |
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#2: Protein | [ Mass: 35376.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: MMP1356 / Production host: ![]() ![]() |
-Non-polymers , 4 types, 230 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ZN / #4: Chemical | #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.9 % |
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Crystal grow | Temperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: anaerobic conditions (glove box). 0.1M HEPES pH 7.5, 0.2 M ammonium sulfate, 18% (w/v) PEG 4000, 10% isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 7, 2016 / Details: KB mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.980096 Å / Relative weight: 1 |
Reflection | Resolution: 2.79→48.48 Å / Num. obs: 17385 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9 % / Biso Wilson estimate: 94.14 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.183 / Rpim(I) all: 0.088 / Rrim(I) all: 0.194 / Rsym value: 0.183 / Χ2: 1.04 / Net I/av σ(I): 7.5 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.79→2.86 Å / Redundancy: 9 % / Rmerge(I) obs: 6.89 / Mean I/σ(I) obs: 0.3 / Num. unique obs: 1150 / CC1/2: 0.146 / Rpim(I) all: 2.366 / Rrim(I) all: 7.304 / Rsym value: 6.89 / Χ2: 0.69 / % possible all: 91.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3VRH Resolution: 2.81→31.85 Å / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.561
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Displacement parameters | Biso mean: 99.04 Å2
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Refine analyze | Luzzati coordinate error obs: 0.42 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.81→31.85 Å
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LS refinement shell | Resolution: 2.81→2.97 Å
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