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- PDB-2eif: Eukaryotic translation initiation factor 5A from Methanococcus ja... -

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Basic information

Entry
Database: PDB / ID: 2eif
TitleEukaryotic translation initiation factor 5A from Methanococcus jannaschii
ComponentsPROTEIN (EUKARYOTIC TRANSLATION INITIATION FACTOR 5A)
KeywordsGENE REGULATION / EIF-5A / TRANSLATION / OB-FOLD / Structural Genomics / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKim, K.K. / Hung, L.W. / Kim, R. / Kim, S.H. / Berkeley Structural Genomics Center (BSGC)
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
DepositionOct 12, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 12, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (EUKARYOTIC TRANSLATION INITIATION FACTOR 5A)


Theoretical massNumber of molelcules
Total (without water)14,6531
Polymers14,6531
Non-polymers00
Water1,946108
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.483, 40.198, 48.580
Angle α, β, γ (deg.)90.00, 124.29, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PROTEIN (EUKARYOTIC TRANSLATION INITIATION FACTOR 5A) / IF-5A


Mass: 14653.239 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: DSM 2661 / 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.: 108 / 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: 2.22 Å3/Da / Density % sol: 45 %
Crystal growpH: 8.5 / Details: 0.1M TRIS-HCL (PH 8.5), 0.2M MGCL2, 30% PEG4000
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
20.1 MTris-HCl1drop
30.2 M1dropMgCl2
430 %PEG40001drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONNSLS X4A1
SYNCHROTRONNSLS X12B2
ROTATING ANODERIGAKU31.54
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jul 1, 1997 / Details: MSC FOCUSING MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 11659 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 1.98 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 16.2
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.233 / Mean I/σ(I) obs: 3.7 / Rsym value: 0.233 / % possible all: 91.2

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Processing

Software
NameVersionClassification
CCP4model building
CNS0.3refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EIF

1eif


Resolution: 1.8→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high rms absF: 1097804.99 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1185 10.3 %RANDOM
Rwork0.214 ---
obs0.214 11482 95.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.9 Å2 / ksol: 0.397 e/Å3
Displacement parametersBiso mean: 25.3 Å2
Baniso -1Baniso -2Baniso -3
1-4.74 Å20 Å24.88 Å2
2---4.14 Å20 Å2
3----0.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms992 0 0 108 1100
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.021.5
X-RAY DIFFRACTIONc_mcangle_it4.062
X-RAY DIFFRACTIONc_scbond_it21.032
X-RAY DIFFRACTIONc_scangle_it14.82.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.342 218 11.9 %
Rwork0.285 1621 -
obs--93.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 10.3 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.89
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.342 / % reflection Rfree: 11.9 % / Rfactor Rwork: 0.285

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