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- PDB-3er0: Crystal structure of the full length eIF5A from Saccharomyces cer... -

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Basic information

Entry
Database: PDB / ID: 3er0
TitleCrystal structure of the full length eIF5A from Saccharomyces cerevisiae
ComponentsEukaryotic translation initiation factor 5A-2
KeywordsTRANSLATION / translation initiation factor / yeast / low resolution / Acetylation / Hypusine / Initiation factor / Phosphoprotein / Protein biosynthesis
Function / homology
Function and homology information


positive regulation of cytoplasmic translational elongation through polyproline stretches / Hypusine synthesis from eIF5A-lysine / CAT tailing / translational frameshifting / positive regulation of translational termination / positive regulation of translational elongation / translational elongation / positive regulation of translational initiation / translation elongation factor activity / translation initiation factor activity ...positive regulation of cytoplasmic translational elongation through polyproline stretches / Hypusine synthesis from eIF5A-lysine / CAT tailing / translational frameshifting / positive regulation of translational termination / positive regulation of translational elongation / translational elongation / positive regulation of translational initiation / translation elongation factor activity / translation initiation factor activity / rescue of stalled ribosome / ribosome binding / perinuclear region of cytoplasm / mitochondrion / RNA binding / cytoplasm
Similarity search - Function
: / 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 ...: / 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
Eukaryotic translation initiation factor 5A-1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsSanches, M. / Dias, C.A.O. / Aponi, L.H. / Valentini, S.R. / Guimaraes, B.
CitationJournal: To be Published
Title: Crystal structure of the full length eIF5A from Saccharomyces cerevisiae
Authors: Sanches, M. / Dias, C.A.O. / Aponi, L.H. / Valentini, S.R. / Guimaraes, B.
History
DepositionOct 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,7952
Polymers36,7952
Non-polymers00
Water00
1
A: Eukaryotic translation initiation factor 5A-2


Theoretical massNumber of molelcules
Total (without water)18,3981
Polymers18,3981
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Eukaryotic translation initiation factor 5A-2


Theoretical massNumber of molelcules
Total (without water)18,3981
Polymers18,3981
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.664, 59.664, 339.790
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 1 / Auth seq-ID: 17 - 151 / Label seq-ID: 27 - 161

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Eukaryotic translation initiation factor 5A-2 / eIF-5A-2 / eIF-4D / Hypusine-containing protein HP2


Mass: 18397.697 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HYP2, TIF51A, YEL034W, SYGP-ORF21 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: P23301

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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: 2.37 Å3/Da / Density % sol: 48.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES, 30% PEG400, 0.1M MgCl2, 3% Glicerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.427 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 1, 2006
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.427 Å / Relative weight: 1
ReflectionResolution: 3.35→49.45 Å / Num. obs: 5431 / % possible obs: 92.1 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.082
Reflection shellResolution: 3.35→3.53 Å / Redundancy: 6 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.6 / % possible all: 89.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1X6O

1x6o


Resolution: 3.35→49.45 Å / Cor.coef. Fo:Fc: 0.839 / Cor.coef. Fo:Fc free: 0.744 / SU B: 74.576 / SU ML: 1.256 / Cross valid method: THROUGHOUT / ESU R Free: 1.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.44824 528 9.9 %RANDOM
Rwork0.38555 ---
obs0.3916 4815 91.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 84.487 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20.29 Å20 Å2
2--0.59 Å20 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 3.35→49.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2105 0 0 0 2105
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222132
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1491.9832865
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg22.0065274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.06826.04786
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.22615408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.864157
X-RAY DIFFRACTIONr_chiral_restr0.1690.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021545
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2970.21262
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21403
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.220.293
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3230.275
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4210.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1351.51407
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.22922210
X-RAY DIFFRACTIONr_scbond_it0.2873787
X-RAY DIFFRACTIONr_scangle_it0.4574.5655
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1001 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.080.05
tight thermal0.090.5
LS refinement shellResolution: 3.35→3.439 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 36 -
Rwork0.385 331 -
obs--91.07 %

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