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- PDB-3dkp: Human DEAD-box RNA-helicase DDX52, conserved domain I in complex ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3dkp | ||||||
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Title | Human DEAD-box RNA-helicase DDX52, conserved domain I in complex with ADP | ||||||
![]() | Probable ATP-dependent RNA helicase DDX52 | ||||||
![]() | HYDROLASE / RNA HELICASE / DEAD / ADP / Structural Genomics / Structural Genomics Consortium / SGC / rRNA / ATP-binding / Nucleotide-binding / Nucleus / Phosphoprotein / RNA-binding | ||||||
Function / homology | ![]() rRNA modification in the nucleus and cytosol / Major pathway of rRNA processing in the nucleolus and cytosol / maturation of SSU-rRNA / rRNA processing / RNA helicase activity / RNA helicase / nucleolus / RNA binding / nucleoplasm / ATP binding / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lehtio, L. / Karlberg, T. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. ...Lehtio, L. / Karlberg, T. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Kotenyova, T. / Moche, M. / Nilsson, M.E. / Nordlund, P. / Nyman, T. / Olesen, K. / Persson, C. / Sagemark, J. / Thorsell, A.G. / Tresaugues, L. / van den Berg, S. / Welin, M. / Wisniewska, M. / Wikstrom, M. / Schueler, H. / 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 | ![]() | 67.9 KB | Display | ![]() |
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PDB format | ![]() | 47.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 13.2 KB | Display | |
Data in CIF | ![]() | 18.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2g9nC ![]() 2p6nC ![]() 2pl3C ![]() 2rb4C ![]() 3b7gC ![]() 3berC ![]() 3borC ![]() 3fe2C ![]() 3iuyC ![]() 3ly5C ![]() 2db3S 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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Unit cell |
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Components
#1: Protein | Mass: 27432.959 Da / Num. of mol.: 1 / Fragment: Conserved domain I: Residues 139-381 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9Y2R4, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides | ||||
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#2: Chemical | ChemComp-MG / | ||||
#3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.36 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 10% PEG 8000, 100 mM Imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 22, 2008 / Details: Mirrors |
Radiation | Monochromator: Silicon (111) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. all: 13480 / Num. obs: 13480 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.65 % / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 3.68 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 4.61 / Num. unique all: 1731 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2DB3 Resolution: 2.1→19.56 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.908 / SU B: 11.364 / SU ML: 0.138 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic + TLS groups / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.269 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.348 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→19.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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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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