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Open data
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Basic information
Entry | Database: PDB / ID: 1xly | ||||||
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Title | X-RAY STRUCTURE OF THE RNA-BINDING PROTEIN SHE2p | ||||||
![]() | SHE2p | ||||||
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Function / homology | ![]() mating type switching / intracellular mRNA localization / cellular bud tip / sequence-specific mRNA binding / mRNA transport / ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Niessing, D. / Huettelmaier, S. / Zenklusen, D. / Singer, R.H. / Burley, S.K. | ||||||
![]() | ![]() Title: She2p is a novel RNA binding protein with a basic helical hairpin motif Authors: Niessing, D. / Huettelmaier, S. / Zenklusen, D. / Singer, R.H. / Burley, S.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 101.1 KB | Display | ![]() |
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PDB format | ![]() | 78.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | The biological assembly is a dimer of non-crystallographic symmetry |
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Components
#1: Protein | Mass: 26807.252 Da / Num. of mol.: 2 / Mutation: C14S, C68, C106S, C180S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: SHE2, YKL130C / Plasmid: pGEX-6P1 / Production host: ![]() ![]() ![]() #2: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49 % |
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Crystal grow![]() | Temperature: 293 K / pH: 8.5 Details: PEG 4000, lithium sulfate, tris, beta-octyl-glucoside, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 23, 2003 |
Radiation | Monochromator: DIAMOND 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.95→25 Å / Num. obs: 37528 / % possible obs: 98 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 24.1 Å2 / Rsym value: 0.086 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.95→2.02 Å / Mean I/σ(I) obs: 2.7 / Rsym value: 0.486 / % possible all: 97.2 |
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Processing
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Refinement | Method to determine structure![]() ![]() Details: PHE 176 in CHAIN B has very high B values and is close to the end of a short helix. It is well possible, that this residue adopts different conformations in the various molecules of the ...Details: PHE 176 in CHAIN B has very high B values and is close to the end of a short helix. It is well possible, that this residue adopts different conformations in the various molecules of the asymmetric, so that in reality the reported clashes are avoided. The high B values and the weak visible electron density prevent a clear observation in this regard. We, therefore, chose to refine a conformation that is most consistent with the visible density and conforms with stereochemical requirements. It is also worth mentioning that, for the second molecule of this homodimer (CHAIN A), this region shows much stronger electron density. The structural model of CHAIN A, therefore, gives a very clear, and much better, description of this region. Consistently, we show in our publication a symmetry operated homodimer consisting of two CHAIN A models.
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Displacement parameters | Biso mean: 44.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→19.76 Å
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Refine LS restraints |
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