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- PDB-5hy6: Spodoptera frugiperda eukaryotic translation initiation factor EIF5A -

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Basic information

Entry
Database: PDB / ID: 5hy6
TitleSpodoptera frugiperda eukaryotic translation initiation factor EIF5A
ComponentsEukaryotic translation initiation factor 5A
KeywordsTRANSLATION / ribosome binding translation elongation factor activity
Function / homology
Function and homology information


positive regulation of translational termination / positive regulation of translational elongation / translation elongation factor activity / ribosome binding / cytoplasm
Similarity search - Function
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 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
Eukaryotic translation initiation factor 5A
Similarity search - Component
Biological speciesSpodoptera frugiperda (fall armyworm)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.186 Å
AuthorsLi, A.W.H. / Oliver, A.W. / Pearl, L.H.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: To Be Published
Title: Structure of Spodoptera frugiperda eukaryotic translation initiation factor EIF5A
Authors: Li, A.W.H. / Oliver, A.W. / Pearl, L.H.
History
DepositionFeb 1, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs
Revision 1.2Jan 10, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)17,5501
Polymers17,5501
Non-polymers00
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.780, 56.780, 87.421
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Eukaryotic translation initiation factor 5A / eIF-5A


Mass: 17549.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spodoptera frugiperda (fall armyworm) / References: UniProt: P62925
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.32 Å3/Da / Density % sol: 46.94 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: Ammonium chloride, MES, PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.186→27.002 Å / Num. obs: 8318 / % possible obs: 99.9 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.256 / Net I/σ(I): 6.9
Reflection shellResolution: 2.19→2.25 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
iMOSFLMdata reduction
Aimless1.10.13data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CPF

3cpf


Resolution: 2.186→27.002 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.08
RfactorNum. reflection% reflection
Rfree0.2595 411 4.96 %
Rwork0.2052 --
obs0.2077 8285 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.186→27.002 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1078 0 0 58 1136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011094
X-RAY DIFFRACTIONf_angle_d1.051471
X-RAY DIFFRACTIONf_dihedral_angle_d19.676673
X-RAY DIFFRACTIONf_chiral_restr0.057167
X-RAY DIFFRACTIONf_plane_restr0.005191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1863-2.50250.30021410.2562600X-RAY DIFFRACTION100
2.5025-3.15210.30821370.24262622X-RAY DIFFRACTION100
3.1521-27.00380.22371330.17592652X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.65970.49140.70321.96061.66722.44770.1533-1.49350.97650.4866-0.45580.0822-0.0074-0.71770.02990.2761-0.05440.10370.574-0.39750.4762-19.424621.404432.0591
21.6587-0.85660.02955.3411-3.07251.8947-0.36730.5122-0.8588-0.4470.0897-0.05781.01760.55440.28371.414-0.02450.34291.9179-0.1710.9381-24.25734.131647.9852
31.62180.4323-0.29314.70922.3862.9820.0656-1.45351.67740.5642-0.79971.0482-0.1269-0.94760.16820.4061-0.05190.09210.8036-0.41610.6184-23.721922.583631.7625
45.41120.5111.15975.06780.84471.4671-0.04530.2030.1168-0.4720.1484-0.26360.00410.16330.07830.23680.02540.00930.14420.00730.2241-16.10516.488610.2996
54.64810.26220.48017.08231.27295.4203-0.05630.48880.2102-0.3339-0.19840.7440.0295-0.16820.2060.2163-0.01520.00780.1878-0.00880.2362-22.52833.8348.7693
63.82350.78760.59294.40651.15065.217-0.12870.54460.2321-1.17470.04050.3856-0.05730.24840.17850.473-0.0335-0.01660.20290.01650.2785-19.165212.65835.7151
70.255-0.13910.071.85051.89622.3322-0.0990.0273-0.2829-0.6016-0.1249-0.2547-0.05270.4130.16470.3180.01240.03150.2865-0.00690.3346-16.331312.086510.2868
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 46 )
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 57 )
3X-RAY DIFFRACTION3chain 'A' and (resid 58 through 86 )
4X-RAY DIFFRACTION4chain 'A' and (resid 87 through 96 )
5X-RAY DIFFRACTION5chain 'A' and (resid 97 through 119 )
6X-RAY DIFFRACTION6chain 'A' and (resid 120 through 145 )
7X-RAY DIFFRACTION7chain 'A' and (resid 146 through 156 )

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