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- PDB-1i8f: THE CRYSTAL STRUCTURE OF A HEPTAMERIC ARCHAEAL SM PROTEIN: IMPLIC... -

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Basic information

Entry
Database: PDB / ID: 1i8f
TitleTHE CRYSTAL STRUCTURE OF A HEPTAMERIC ARCHAEAL SM PROTEIN: IMPLICATIONS FOR THE EUKARYOTIC SNRNP CORE
ComponentsPUTATIVE SNRNP SM-LIKE PROTEIN
KeywordsSTRUCTURAL GENOMICS / beta barrel-like SmAP monomers form 35-stranded beta-sheet in the heptamer
Function / homology
Function and homology information


mRNA processing / ribonucleoprotein complex / RNA binding
Similarity search - Function
snRNP Sm-like, putative, archaea / U6 snRNA-associated Sm-like protein Lsm1/8 / SH3 type barrels. - #100 / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM domain superfamily / SH3 type barrels. ...snRNP Sm-like, putative, archaea / U6 snRNA-associated Sm-like protein Lsm1/8 / SH3 type barrels. - #100 / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Putative snRNP Sm-like protein
Similarity search - Component
Biological speciesPyrobaculum aerophilum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsMura, C. / Cascio, D. / Sawaya, M.R. / Eisenberg, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: The crystal structure of a heptameric archaeal Sm protein: Implications for the eukaryotic snRNP core.
Authors: Mura, C. / Cascio, D. / Sawaya, M.R. / Eisenberg, D.S.
History
DepositionMar 14, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 21, 2021Group: Data collection / Derived calculations / Refinement description
Category: refine / reflns_shell / struct_site
Item: _refine.ls_percent_reflns_obs / _reflns_shell.percent_possible_all ..._refine.ls_percent_reflns_obs / _reflns_shell.percent_possible_all / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PUTATIVE SNRNP SM-LIKE PROTEIN
B: PUTATIVE SNRNP SM-LIKE PROTEIN
C: PUTATIVE SNRNP SM-LIKE PROTEIN
D: PUTATIVE SNRNP SM-LIKE PROTEIN
E: PUTATIVE SNRNP SM-LIKE PROTEIN
F: PUTATIVE SNRNP SM-LIKE PROTEIN
G: PUTATIVE SNRNP SM-LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,02112
Polymers62,5617
Non-polymers4605
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13040 Å2
ΔGint-37 kcal/mol
Surface area20570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.261, 95.738, 62.157
Angle α, β, γ (deg.)90.00, 92.69, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe contents of one asymmetric unit (i.e. a heptamer) most likely correspond to the biologically relevant species for this organism.

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Components

#1: Protein
PUTATIVE SNRNP SM-LIKE PROTEIN


Mass: 8937.272 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum aerophilum (archaea) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8ZYG5
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.38 Å3/Da / Density % sol: 48.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: PEG-4000, acetate, glycerol, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 5, 2000
Details: collimating mirror optics, double-slit monochromator
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.71→100 Å / Num. all: 62547 / Num. obs: 62547 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.48 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 44.4
Reflection shellResolution: 1.71→1.77 Å / Rmerge(I) obs: 0.723 / % possible all: 97.2
Reflection
*PLUS
Rmerge(I) obs: 0.04

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.75→20 Å / Isotropic thermal model: anisotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Each of the seven Sm monomers per a.u. were refined independently in CNS since imposition of restraints or constraints hindered the refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.266 2839 -RANDOM
Rwork0.235 ---
all-59011 --
obs-56641 96 %-
Displacement parametersBiso mean: 38.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3815 0 30 130 3975
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01809
X-RAY DIFFRACTIONc_angle_deg1.8962
X-RAY DIFFRACTIONc_dihedral_angle_d26.232
X-RAY DIFFRACTIONc_improper_angle_d1.2245
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.235
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 38.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.232
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.2245

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