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Yorodumi- PDB-3ber: Human DEAD-box RNA-helicase DDX47, conserved domain I in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ber | ||||||
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Title | Human DEAD-box RNA-helicase DDX47, conserved domain I in complex with AMP | ||||||
Components | Probable ATP-dependent RNA helicase DDX47 | ||||||
Keywords | HYDROLASE / RNA HELICASE / DEAD / AMP / Structural Genomics / Structural Genomics Consortium / SGC / ATP-binding / Nucleotide-binding / Nucleus / RNA-binding | ||||||
Function / homology | Function and homology information rRNA modification in the nucleus and cytosol / extrinsic apoptotic signaling pathway via death domain receptors / Major pathway of rRNA processing in the nucleolus and cytosol / RNA splicing / mRNA processing / rRNA processing / RNA helicase activity / RNA helicase / nucleolus / RNA binding ...rRNA modification in the nucleus and cytosol / extrinsic apoptotic signaling pathway via death domain receptors / Major pathway of rRNA processing in the nucleolus and cytosol / RNA splicing / mRNA processing / rRNA processing / RNA helicase activity / RNA helicase / nucleolus / RNA binding / nucleoplasm / ATP binding / membrane / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Karlberg, T. / Busam, R.D. / Arrowsmith, C.H. / Berglund, H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Karlberg, T. / Busam, R.D. / Arrowsmith, C.H. / Berglund, H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Kallas, A. / Kotenyova, T. / Lehtio, L. / Moche, M. / Nilsson, M.E. / Nordlund, P. / Nyman, T. / Persson, C. / Sagemark, J. / Svensson, L. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Holmberg-Schiavone, L. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Plos One / Year: 2010 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ber.cif.gz | 68.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ber.ent.gz | 47.8 KB | Display | PDB format |
PDBx/mmJSON format | 3ber.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/3ber ftp://data.pdbj.org/pub/pdb/validation_reports/be/3ber | HTTPS FTP |
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-Related structure data
Related structure data | 2g9nC 2p6nC 2pl3C 2rb4C 3b7gC 3borC 3dkpC 3fe2C 3iuyC 3ly5C 2gxsS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 27460.580 Da / Num. of mol.: 1 / Fragment: Conserved domain I (DEAD): Residues 5-230 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DDX47 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)gold pRARE2 References: UniProt: Q9H0S4, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides | ||
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#2: Chemical | ChemComp-PO4 / | ||
#3: Chemical | ChemComp-AMP / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.46 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.2 Details: 42.5% PEG 200, 100mM Sodium/potassium phosphate, 50mM Sodium chloride, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97472 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 25, 2007 Details: liquid nitrogen cooled channel-cut silicon monochromator and a cylindrical grazing incidence mirror |
Radiation | Monochromator: Si(311) and Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97472 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→30 Å / Num. all: 45260 / Num. obs: 45260 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.052 / Rsym value: 0.029 / Net I/σ(I): 28.7 |
Reflection shell | Resolution: 1.4→1.5 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.141 / Mean I/σ(I) obs: 14.1 / Num. unique all: 8478 / Rsym value: 0.082 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2GXS Resolution: 1.4→28.24 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.956 / SU B: 0.833 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.059 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.83 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→28.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
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