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Yorodumi- PDB-2pl3: Human DEAD-box RNA helicase DDX10, DEAD domain in complex with ADP -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pl3 | ||||||
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Title | Human DEAD-box RNA helicase DDX10, DEAD domain in complex with ADP | ||||||
Components | Probable ATP-dependent RNA helicase DDX10 | ||||||
Keywords | HYDROLASE / RNA / HELICASE / DEAD / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC | ||||||
Function / homology | Function and homology information anterior head development / rRNA processing / RNA helicase activity / RNA helicase / RNA binding / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Karlberg, T. / Lehtio, L. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. ...Karlberg, T. / Lehtio, L. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. / Graslund, S. / Hallberg, B.M. / Hammarstrom, M. / Johansson, I. / Kallas, A. / Kotenyova, T. / Moche, M. / Nordlund, P. / Nyman, T. / Persson, C. / Sagemark, J. / Stenmark, P. / Sundstrom, M. / Thorsell, A.G. / Van Den Berg, S. / Weigelt, J. / 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 | 2pl3.cif.gz | 64.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pl3.ent.gz | 45.7 KB | Display | PDB format |
PDBx/mmJSON format | 2pl3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2pl3_validation.pdf.gz | 882.7 KB | Display | wwPDB validaton report |
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Full document | 2pl3_full_validation.pdf.gz | 888.7 KB | Display | |
Data in XML | 2pl3_validation.xml.gz | 12 KB | Display | |
Data in CIF | 2pl3_validation.cif.gz | 16 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pl/2pl3 ftp://data.pdbj.org/pub/pdb/validation_reports/pl/2pl3 | HTTPS FTP |
-Related structure data
Related structure data | 2g9nC 2p6nC 2rb4C 3b7gC 3berC 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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Details | The monomer in the ASU is the biological assembly |
-Components
#1: Protein | Mass: 26590.709 Da / Num. of mol.: 1 / Fragment: DEAD domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DDX10 / Plasmid: pNIC-BSA4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) GOLD PRARE2 References: UniProt: Q13206, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides | ||
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#2: Chemical | ChemComp-MG / | ||
#3: Chemical | ChemComp-ADP / | ||
#4: Chemical | ChemComp-EOH / #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: 3.33 Å3/Da / Density % sol: 63.02 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 20% Ethanol, 50mM Sodium chloride, 100mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04123 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 22, 2007 / Details: Multilayer mirror |
Radiation | Monochromator: Bent germanium crystal, horizontal focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04123 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→30 Å / Num. all: 20889 / Num. obs: 20889 / % possible obs: 99.7 % / Redundancy: 25.4 % / Rmerge(I) obs: 0.048 / Rsym value: 0.017 / Net I/σ(I): 54.1 |
Reflection shell | Resolution: 2.15→2.3 Å / Redundancy: 26.5 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 24.5 / Num. unique all: 3719 / Rsym value: 0.047 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2GXS Resolution: 2.15→29.3 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.914 / SU B: 7.234 / SU ML: 0.106 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.168 / 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: 38.392 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→29.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.206 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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