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- PDB-1xly: X-RAY STRUCTURE OF THE RNA-BINDING PROTEIN SHE2p -

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Basic information

Entry
Database: PDB / ID: 1xly
TitleX-RAY STRUCTURE OF THE RNA-BINDING PROTEIN SHE2p
ComponentsSHE2p
KeywordsRNA 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 / cytoplasm / cytosol
Similarity search - Function
She2 domain / RNA binding protein She2 / She2 domain superfamily / RNA binding protein She2p / Fumarase C; Chain A, domain 2 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
SWI5-dependent HO expression protein 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.95 Å
AuthorsNiessing, D. / Huettelmaier, S. / Zenklusen, D. / Singer, R.H. / Burley, S.K.
CitationJournal: 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
DepositionSep 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 3, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.5Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SHE2p
B: SHE2p


Theoretical massNumber of molelcules
Total (without water)53,6152
Polymers53,6152
Non-polymers00
Water5,441302
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.199, 103.647, 56.733
Angle α, β, γ (deg.)90.00, 110.51, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a dimer of non-crystallographic symmetry

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Components

#1: Protein SHE2p / SHE2 / YKL130C


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 / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 293 K / pH: 8.5
Details: PEG 4000, lithium sulfate, tris, beta-octyl-glucoside, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 1.072
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 23, 2003
RadiationMonochromator: DIAMOND 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameClassification
REFMACrefinement
MAR345data collection
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod 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.
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1898 5 %RANDOM
Rwork0.191 ---
obs0.206 37528 98 %-
all-37528 --
Displacement parametersBiso mean: 44.5 Å2
Refinement stepCycle: LAST / Resolution: 1.95→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3327 0 0 302 3629
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0271.5
X-RAY DIFFRACTIONp_angle_d2.32
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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