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- PDB-2g9n: Structure of the DEAD domain of Human eukaryotic initiation facto... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2g9n | ||||||
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Title | Structure of the DEAD domain of Human eukaryotic initiation factor 4A, eIF4A | ||||||
![]() | Eukaryotic initiation factor 4A-I | ||||||
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Function / homology | ![]() Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hogbom, M. / Ogg, D. / Arrowsmith, C. / Berglund, H. / Collins, R. / Edwards, A. / Ehn, M. / Flodin, S. / Flores, A. / Graslund, S. ...Hogbom, M. / Ogg, D. / Arrowsmith, C. / Berglund, H. / Collins, R. / Edwards, A. / Ehn, M. / Flodin, S. / Flores, A. / Graslund, S. / Hallberg, B.M. / Hammarstrom, M. / Kotenyova, T. / Nilsson-Ehle, P. / Nordlund, P. / Nyman, T. / Persson, C. / Sagemark, J. / Stenmark, P. / Sundstrom, M. / Thorsell, A.G. / Uppenberg, J. / Van Den Berg, S. / Weigelt, J. / Holmberg-Schiavone, L. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Comparative Structural Analysis of Human DEAD-Box RNA Helicases. Authors: Schutz, P. / Karlberg, T. / van den Berg, S. / Collins, R. / Lehtio, L. / Hogbom, M. / Holmberg-Schiavone, L. / Tempel, W. / Park, H.W. / Hammarstrom, M. / Moche, M. / Thorsell, A.G. / Schuler, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 104.5 KB | Display | ![]() |
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PDB format | ![]() | 81.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2p6nC ![]() 2pl3C ![]() 2rb4C ![]() 3b7gC ![]() 3berC ![]() 3borC ![]() 3dkpC ![]() 3fe2C ![]() 3iuyC ![]() 3ly5C ![]() 1qdeS S: Starting model for refinement C: citing same article ( |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 4
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Components
#1: Protein | Mass: 25087.316 Da / Num. of mol.: 2 / Fragment: DEAD domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P60842, ![]() #2: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.56 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% PEG3350, 200 mM Ammonium Nitrate, 500 mM NaCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 12, 2006 |
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.25→20 Å / Num. all: 19100 / Num. obs: 19100 / % possible obs: 99.65 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.45 % / Biso Wilson estimate: 25.9 Å2 / Rsym value: 0.071 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.25→2.37 Å / Redundancy: 3.46 % / Mean I/σ(I) obs: 5.3 / Num. unique all: 2912 / Rsym value: 0.241 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: pdb entry 1QDE Resolution: 2.25→20 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.882 / SU B: 12.622 / SU ML: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.365 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.89 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1514 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.25→2.308 Å / Total num. of bins used: 20
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