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- PDB-1eif: EUKARYOTIC TRANSLATION INITIATION FACTOR 5A FROM METHANOCOCCUS JA... -

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Basic information

Entry
Database: PDB / ID: 1eif
TitleEUKARYOTIC TRANSLATION INITIATION FACTOR 5A FROM METHANOCOCCUS JANNASCHII
ComponentsEUKARYOTIC TRANSLATION INITIATION FACTOR 5A
KeywordsINITIATION FACTOR / EIF-5A / TRANSLATION / OB-FOLD
Function / homology
Function and homology information


positive regulation of translational termination / positive regulation of translational elongation / translational elongation / translation elongation factor activity / translation initiation factor activity / ribosome binding / RNA binding / cytoplasm
Similarity search - Function
Translation elongation factor IF5A, archaeal / Elongation factor P (EF-P) KOW-like domain / : / Translation initiation factor 5A-like, N-terminal / Translation elongation factor, IF5A, hypusine site / Eukaryotic initiation factor 5A hypusine signature. / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / Translation elongation factor IF5A-like / Translation elongation factor, IF5A C-terminal / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold ...Translation elongation factor IF5A, archaeal / Elongation factor P (EF-P) KOW-like domain / : / Translation initiation factor 5A-like, N-terminal / Translation elongation factor, IF5A, hypusine site / Eukaryotic initiation factor 5A hypusine signature. / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / Translation elongation factor IF5A-like / Translation elongation factor, IF5A C-terminal / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / SH3 type barrels. - #30 / Nucleic acid-binding proteins / SH3 type barrels. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Translation protein SH3-like domain superfamily / Ribosomal protein L2, domain 2 / Roll / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Translation initiation factor 5A
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR, MAD / Resolution: 1.9 Å
AuthorsKim, K.K. / Hung, L.W. / Yokota, H. / Kim, R. / Kim, S.H.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Crystal structures of eukaryotic translation initiation factor 5A from Methanococcus jannaschii at 1.8 A resolution.
Authors: Kim, K.K. / Hung, L.W. / Yokota, H. / Kim, R. / Kim, S.H.
#1: Journal: Protein Sci. / Year: 1997
Title: Cloning, Expression, and Crystallization of a Hyperthermophilic Protein that is Homologous to the Eukaryotic Translation Initiation Factor, Eif5A
Authors: Kim, K.K. / Yokota, H. / Kim, R. / Kim, S.H.
History
DepositionJul 29, 1998Processing site: BNL
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EUKARYOTIC TRANSLATION INITIATION FACTOR 5A


Theoretical massNumber of molelcules
Total (without water)14,5221
Polymers14,5221
Non-polymers00
Water1,71195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.520, 45.520, 155.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-192-

HOH

21A-215-

HOH

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Components

#1: Protein EUKARYOTIC TRANSLATION INITIATION FACTOR 5A


Mass: 14522.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Cell line: BL21 / Plasmid: PET21A/PSJS1240 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q58625
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.76 Å3/Da / Density % sol: 55 %
Crystal growpH: 4.6 / Details: 0.1 M SODIUM ACETATE (PH 4.6) 8% PEK4000
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
20.1 Msodium acetate1drop
38 %(w/v)PEG40001drop

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.95
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1997 / Details: 1\:1 DEFOCUSED RHODIUM-COATED SILICON CARBIDE
RadiationMonochromator: DOUBLE FLAT CRYSTAL FIXED-EXIT MONOCHROMATOR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 12622 / % possible obs: 92.3 % / Redundancy: 4.02 % / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 24.1
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 5.3 / Rsym value: 0.326 / % possible all: 97.7

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Processing

Software
NameVersionClassification
X-PLOR3.85model building
X-PLOR3.85refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.85phasing
RefinementMethod to determine structure: MIR, MAD / Resolution: 1.9→6 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: FREE-R / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.289 2202 10 %RANDOM
Rwork0.205 ---
obs0.205 11639 88.4 %-
Displacement parametersBiso mean: 45 Å2
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms965 0 0 96 1061
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.547
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d30.03
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.921
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.1551.5
X-RAY DIFFRACTIONx_mcangle_it3.6852
X-RAY DIFFRACTIONx_scbond_it3.5042
X-RAY DIFFRACTIONx_scangle_it5.6312.5
LS refinement shellResolution: 1.9→1.98 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.338 117 7.3 %
Rwork0.31 1220 -
obs--79.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.85 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg30.03
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.921
LS refinement shell
*PLUS
Rfactor Rwork: 0.31

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