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- PDB-3hks: Crystal structure of eukaryotic translation initiation factor eIF... -

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Basic information

Entry
Database: PDB / ID: 3hks
TitleCrystal structure of eukaryotic translation initiation factor eIF-5A2 from Arabidopsis thaliana
ComponentsEukaryotic translation initiation factor 5A-2
KeywordsTRANSLATION / RNA BINDING PROTEIN / BETA BARREL / Alternative splicing / Hypusine / Initiation factor / Protein biosynthesis
Function / homology
Function and homology information


positive regulation of translational termination / positive regulation of translational elongation / symbiont-induced defense-related programmed cell death / programmed cell death / translation elongation factor activity / response to cadmium ion / translational initiation / translation initiation factor activity / response to bacterium / response to wounding ...positive regulation of translational termination / positive regulation of translational elongation / symbiont-induced defense-related programmed cell death / programmed cell death / translation elongation factor activity / response to cadmium ion / translational initiation / translation initiation factor activity / response to bacterium / response to wounding / ribosome binding / defense response to bacterium / nucleus / cytosol
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-2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTeng, Y.B. / He, Y.X. / Jiang, Y.L. / Chen, Y.X. / Zhou, C.Z.
CitationJournal: Proteins / Year: 2009
Title: Crystal structure of Arabidopsis translation initiation factor eIF-5A2
Authors: Teng, Y.-B. / Ma, X.-X. / He, Y.-X. / Jiang, Y.-L. / Du, J. / Xiang, C. / Chen, Y. / Zhou, C.-Z.
History
DepositionMay 25, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Eukaryotic translation initiation factor 5A-2
B: Eukaryotic translation initiation factor 5A-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7398
Polymers36,3672
Non-polymers3726
Water3,045169
1
A: Eukaryotic translation initiation factor 5A-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4325
Polymers18,1831
Non-polymers2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Eukaryotic translation initiation factor 5A-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3083
Polymers18,1831
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.560, 79.830, 94.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Eukaryotic translation initiation factor 5A-2 / eIF-5A-2


Mass: 18183.420 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1G26630.1 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 DE3 / References: UniProt: Q93VP3
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.95 Å3/Da / Density % sol: 58.26 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 6, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.23→94.92 Å / Num. obs: 20393 / % possible obs: 99.5 % / Rmerge(I) obs: 0.066
Reflection shellResolution: 2.23→2.28 Å

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASESphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1x6o

1x6o


Resolution: 2.3→94.92 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.912 / SU B: 5.041 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.241 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24074 1183 6 %RANDOM
Rwork0.20201 ---
obs0.20435 18539 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.554 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å20 Å20 Å2
2--1.66 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 2.3→94.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2163 0 24 169 2356
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222214
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2661.9662972
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2455286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.225.50689
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.58815403
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.012158
X-RAY DIFFRACTIONr_chiral_restr0.0860.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021612
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.2794
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2930.21470
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2146
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.261
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2210.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2241.51475
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.31522292
X-RAY DIFFRACTIONr_scbond_it2.1273823
X-RAY DIFFRACTIONr_scangle_it3.5334.5680
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 85 -
Rwork0.215 1326 -
obs--98.81 %

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