+Open data
-Basic information
Entry | Database: PDB / ID: 1xly | ||||||
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Title | X-RAY STRUCTURE OF THE RNA-BINDING PROTEIN SHE2p | ||||||
Components | SHE2p | ||||||
Keywords | RNA BINDING PROTEIN / basic helical hairpin / five helix bundle / dimer / RNA-BINDING PROTEIN | ||||||
Function / homology | Function and homology information mating type switching / cellular bud tip / intracellular mRNA localization / sequence-specific mRNA binding / mRNA transport / mRNA binding / lipid binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.95 Å | ||||||
Authors | Niessing, D. / Huettelmaier, S. / Zenklusen, D. / Singer, R.H. / Burley, S.K. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2004 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xly.cif.gz | 101.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xly.ent.gz | 78.3 KB | Display | PDB format |
PDBx/mmJSON format | 1xly.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xly_validation.pdf.gz | 436.6 KB | Display | wwPDB validaton report |
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Full document | 1xly_full_validation.pdf.gz | 451.2 KB | Display | |
Data in XML | 1xly_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 1xly_validation.cif.gz | 31.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xl/1xly ftp://data.pdbj.org/pub/pdb/validation_reports/xl/1xly | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Details | The biological assembly is a dimer of non-crystallographic symmetry |
-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.) Saccharomyces cerevisiae (brewer's yeast) Gene: SHE2, YKL130C / Plasmid: pGEX-6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3* / References: UniProt: P36068 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 1.072 |
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: 1.072 Å / Relative weight: 1 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.95→19.76 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber 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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