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- PDB-1nu4: U1A RNA binding domain at 1.8 angstrom resolution reveals a pre-o... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1nu4 | ||||||
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Title | U1A RNA binding domain at 1.8 angstrom resolution reveals a pre-organized C-terminal helix | ||||||
![]() | U1A RNA binding domain | ||||||
![]() | RNA BINDING PROTEIN / RNA recognition motif / U1 small nuclear ribonucleoprotein / RNA binding domain | ||||||
Function / homology | ![]() U1 snRNP binding / U1 snRNP / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / DNA binding / RNA binding / nucleoplasm ...U1 snRNP binding / U1 snRNP / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Rupert, P.B. / Xiao, H. / Ferre-D'Amare, A.R. | ||||||
![]() | ![]() Title: U1A RNA-binding domain at 1.8 A resolution. Authors: Rupert, P.B. / Xiao, H. / Ferre-D'Amare, A.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 58.3 KB | Display | ![]() |
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PDB format | ![]() | 42.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465.3 KB | Display | ![]() |
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Full document | ![]() | 476.5 KB | Display | |
Data in XML | ![]() | 12.8 KB | Display | |
Data in CIF | ![]() | 16.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1urnS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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7 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 11209.120 Da / Num. of mol.: 2 / Fragment: U1A RBD1 / Mutation: Y31H,Q36R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-MLA / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.56 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: Potassium Malonate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.5 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 15, 2002 / Details: osmics mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 18308 / Num. obs: 17618 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 31.1 Å2 / Rmerge(I) obs: 0.031 / Rsym value: 0.031 / Net I/σ(I): 37.6 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 2.46 / Num. unique all: 1365 / Rsym value: 0.311 / % possible all: 76.8 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 70351 |
Reflection shell | *PLUS % possible obs: 76.8 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1urn Resolution: 1.8→29.16 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.9717 Å2 / ksol: 0.401443 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→29.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 30 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.2344 / Rfactor Rwork: 0.2032 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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