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Open data
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Basic information
Entry | Database: PDB / ID: 3els | ||||||
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Title | Crystal Structure of Yeast Pml1p, Residues 51-204 | ||||||
![]() | Pre-mRNA leakage protein 1 | ||||||
![]() | SPLICING / Intrinsically unstructured domain / forkhead-associated domain (FHA) domain / pre-mRNA retention and splicing / protein phosphorylation / RES complex / mRNA processing / mRNA splicing / Nucleus | ||||||
Function / homology | ![]() maintenance of RNA location / RES complex / U2-type prespliceosome assembly / U2 snRNP / mRNA export from nucleus / spliceosomal complex / mRNA splicing, via spliceosome / mRNA binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Trowitzsch, S. / Weber, G. / Luehrmann, R. / Wahl, M.C. | ||||||
![]() | ![]() Title: Crystal structure of the Pml1p subunit of the yeast precursor mRNA retention and splicing complex. Authors: Trowitzsch, S. / Weber, G. / Luhrmann, R. / Wahl, M.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 50 KB | Display | ![]() |
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PDB format | ![]() | 35.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related 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 on special symmetry positions |
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Components
#1: Protein | Mass: 18050.314 Da / Num. of mol.: 1 / Fragment: UNP residues 51 to 204 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: PML1, YLR016C, L1591 / Plasmid: pCDFDuet-1 / Production host: ![]() ![]() | ||
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#2: Chemical | ChemComp-MG / | ||
#3: Chemical | ChemComp-CL / | ||
#4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100 mM Tris-HCl, pH 7.5, 200 mM Li2SO4, 21-24 % PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 1, 2007 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9802 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40.7 Å / Num. obs: 16896 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 71.7 Å2 / Rsym value: 0.083 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 2473 / Rsym value: 0.81 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.309 Å2
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Refine analyze | Luzzati coordinate error obs: 0.21 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.797→1.844 Å / Total num. of bins used: 20
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