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Open data
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Basic information
Entry | Database: PDB / ID: 6nak | ||||||
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Title | BACTERIAL PROTEIN COMPLEX TM BDE complex | ||||||
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![]() | RNA BINDING PROTEIN / HETERO-HEXAMER COMPLEX / METAL ION BINDING PROTEINS | ||||||
Function / homology | ![]() N6-L-threonylcarbamoyladenine synthase / N(6)-L-threonylcarbamoyladenine synthase activity / tRNA threonylcarbamoyladenosine modification / iron ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Stec, B. | ||||||
![]() | ![]() Title: The structure of the TsaB/TsaD/TsaE complex reveals an unexpected mechanism for the bacterial t6A tRNA-modification. Authors: Missoury, S. / Plancqueel, S. / Li de la Sierra-Gallay, I. / Zhang, W. / Liger, D. / Durand, D. / Dammak, R. / Collinet, B. / van Tilbeurgh, H. | ||||||
History |
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Remark 0 | THIS ENTRY 6NAK REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 6FPE, DETERMINED BY S. ...THIS ENTRY 6NAK REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 6FPE, DETERMINED BY S.MISSOURY,S.PLANCQUEEL,I.LI-DE-LA-SIERRA-GALLAY,W.ZHANG,D.LIGER, D.DURAND,R.DAMMAK,B.COLLINET,H.VAN TILBEURGH |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 557.7 KB | Display | ![]() |
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PDB format | ![]() | 459.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6nbjC ![]() 6fpe S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 3 types, 6 molecules ACBGDE
#1: Protein | Mass: 23020.842 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 35672.203 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9WXZ2, N6-L-threonylcarbamoyladenine synthase #3: Protein | Mass: 21513.488 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 12 molecules ![](data/chem/img/TXA.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/APC.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/APC.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.75 % / Description: Author used the sf data from the entry 6FPE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 13 % PEG 8000, 1 mM Imidazole pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 7, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.981 Å / Relative weight: 1 |
Reflection | Resolution: 3.14→48.4 Å / Num. obs: 30297 / % possible obs: 99 % / Redundancy: 4.56 % / Rmerge(I) obs: 0.169 / Net I/σ(I): 7.47 |
Reflection shell | Resolution: 3.14→3.3 Å / Redundancy: 4.7 % / Num. unique obs: 1505 / % possible all: 95 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6fpe ![]() 6fpe Resolution: 3.14→48.4 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.88 / SU B: 78.908 / SU ML: 0.567 / Cross valid method: THROUGHOUT / ESU R Free: 0.598 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 87.322 Å2
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Refinement step | Cycle: 1 / Resolution: 3.14→48.4 Å
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Refine LS restraints |
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