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- PDB-1g62: CRYSTAL STRUCTURE OF S.CEREVISIAE EIF6 -

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Basic information

Entry
Database: PDB / ID: 1g62
TitleCRYSTAL STRUCTURE OF S.CEREVISIAE EIF6
ComponentsRIBOSOME ANTI-ASSOCIATION FACTOR EIF6
KeywordsTRANSLATION / alpha-beta barrel / velcro closure / subdomain / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of 5.8S rRNA / ribosomal large subunit binding / preribosome, large subunit precursor / ribosomal subunit export from nucleus / maturation of LSU-rRNA / translation initiation factor activity / assembly of large subunit precursor of preribosome / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of 5.8S rRNA / ribosomal large subunit binding / preribosome, large subunit precursor / ribosomal subunit export from nucleus / maturation of LSU-rRNA / translation initiation factor activity / assembly of large subunit precursor of preribosome / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome assembly / rRNA processing / nucleolus / nucleus / cytoplasm / cytosol
Similarity search - Function
L-arginine/glycine Amidinotransferase; Chain A / 5-stranded Propeller / L-arginine/glycine Amidinotransferase; Chain A / Translation initiation factor IF6 / eIF-6 family / translation initiation factor 6 / Alpha Beta
Similarity search - Domain/homology
Eukaryotic translation initiation factor 6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGroft, C.M. / Beckmann, R. / Sali, A. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Crystal structures of ribosome anti-association factor IF6.
Authors: Groft, C.M. / Beckmann, R. / Sali, A. / Burley, S.K.
History
DepositionNov 2, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Feb 3, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.6Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIBOSOME ANTI-ASSOCIATION FACTOR EIF6


Theoretical massNumber of molelcules
Total (without water)24,1561
Polymers24,1561
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.257, 56.257, 171.703
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein RIBOSOME ANTI-ASSOCIATION FACTOR EIF6 / EUKARYOTIC TRANSLATION INITIATION FACTOR 6 (EIF-6)


Mass: 24156.150 Da / Num. of mol.: 1 / Mutation: RESIDUES 1-224
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TIF6 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q12522

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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: 2.81 Å3/Da / Density % sol: 56.25 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 2M Ammonium Sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 24.0K
Crystal
*PLUS
Density % sol: 55 %
Crystal grow
*PLUS
Components of the solutions
*PLUS
Conc.: 2 M / Common name: ammonium sulfate

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jul 4, 2000
RadiationMonochromator: Copper / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. all: 9926 / Num. obs: 9926 / % possible obs: 96.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 41.3 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 15.7
Reflection shellResolution: 2.5→25 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.34 / Num. unique all: 836 / % possible all: 84.9
Reflection
*PLUS
Lowest resolution: 25 Å / Num. measured all: 60623
Reflection shell
*PLUS
% possible obs: 84.9 % / Rmerge(I) obs: 0.34

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1G61

1g61


Resolution: 2.5→25 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: CNS-defined values
RfactorNum. reflectionSelection details
Rfree0.25 987 RANDOM
Rwork0.197 --
all-9926 -
obs-9534 -
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1633 0 0 0 1633
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.006
LS refinement shellResolution: 2.5→25 Å
RfactorNum. reflection
Rfree0.25 987
Rwork0.197 -
obs-9534
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 25 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.197 / Rfactor Rfree: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.4
LS refinement shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 25 Å / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.197

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