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Open data
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Basic information
Entry | Database: PDB / ID: 2p6n | ||||||
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Title | Human DEAD-box RNA helicase DDX41, helicase domain | ||||||
![]() | ATP-dependent RNA helicase DDX41 | ||||||
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Function / homology | ![]() STING mediated induction of host immune responses / IRF3-mediated induction of type I IFN / Regulation of innate immune responses to cytosolic DNA / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Karlberg, T. / Ogg, D. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. ...Karlberg, T. / Ogg, D. / 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. / Kotenyova, T. / Lehtio, L. / 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) | ||||||
![]() | ![]() 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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Remark 300 | BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS A MONOMER. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74.7 KB | Display | ![]() |
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PDB format | ![]() | 56 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2g9nC ![]() 2pl3C ![]() 2rb4C ![]() 3b7gC ![]() 3berC ![]() 3borC ![]() 3dkpC ![]() 3fe2C ![]() 3iuyC ![]() 3ly5C ![]() 2i4iS 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: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 5 / Auth seq-ID: 406 - 565 / Label seq-ID: 28 - 187
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Details | The biological unit is a monomer, the asymmetric unit contains two monomers |
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Components
#1: Protein | Mass: 21172.273 Da / Num. of mol.: 2 / Fragment: HELICASE DOMAIN / Mutation: R525C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: Q9UJV9, ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.93 % |
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Crystal grow![]() | Temperature: 293 K / pH: 5.5 Details: 25% PEG 3350, 200mM Lithium sulfate, 100mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 5.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 29, 2006 Details: DOUBLE CRYSTAL, SI(111) OR SI(311), TOROIDAL MIRROR |
Radiation | Monochromator: KHOZU, WITH A MCLENNON CONTROLLER CONTAINING A LN2 COOLED SI111 CRYSTAL Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.6→30 Å / Num. obs: 13827 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 40 % / Rmerge(I) obs: 0.103 / Rsym value: 0.029 / Net I/σ(I): 35.9 |
Reflection shell | Resolution: 2.6→2.8 Å / Redundancy: 41.8 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 12.6 / Rsym value: 0.084 / % possible all: 100 |
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Processing
Software |
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 2I4I Resolution: 2.6→29.72 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.907 / SU B: 27.859 / SU ML: 0.266 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.559 / ESU R Free: 0.337 / 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: 47.341 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→29.72 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.6→2.667 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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