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- PDB-8put: IF5A in complex with Deoxyhypusine synthase -

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Basic information

Entry
Database: PDB / ID: 8put
TitleIF5A in complex with Deoxyhypusine synthase
Components
  • Probable deoxyhypusine synthase
  • Translation initiation factor 5A
KeywordsTRANSLATION / Lysine modification / Hypusine / EIF5A
Function / homology
Function and homology information


deoxyhypusine synthase / deoxyhypusine synthase activity / 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
Deoxyhypusine synthase, putative, archaeal / Translation elongation factor IF5A, archaeal / Deoxyhypusine synthase / Deoxyhypusine synthase superfamily / Deoxyhypusine synthase / : / 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 ...Deoxyhypusine synthase, putative, archaeal / Translation elongation factor IF5A, archaeal / Deoxyhypusine synthase / Deoxyhypusine synthase superfamily / Deoxyhypusine synthase / : / 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 / DHS-like NAD/FAD-binding domain superfamily / Translation protein SH3-like domain superfamily / Ribosomal protein L2, domain 2 / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Probable deoxyhypusine synthase / Translation initiation factor 5A
Similarity search - Component
Biological speciesSulfolobus islandicus (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsEnnifar, E. / D'agostino, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2024
Title: Crystal structure of archaeal IF5A-DHS complex reveals insights into the hypusination mechanism.
Authors: D'Agostino, M. / Simonetti, A. / Motta, S. / Wolff, P. / Romagnoli, A. / Piccinini, A. / Spinozzi, F. / Di Marino, D. / La Teana, A. / Ennifar, E.
History
DepositionJul 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable deoxyhypusine synthase
B: Probable deoxyhypusine synthase
C: Probable deoxyhypusine synthase
D: Probable deoxyhypusine synthase
E: Translation initiation factor 5A
F: Translation initiation factor 5A
G: Translation initiation factor 5A
H: Translation initiation factor 5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,26115
Polymers198,2898
Non-polymers2,9727
Water2,702150
1
A: Probable deoxyhypusine synthase
B: Probable deoxyhypusine synthase
E: Translation initiation factor 5A
F: Translation initiation factor 5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,7909
Polymers99,1444
Non-polymers1,6455
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12320 Å2
ΔGint-52 kcal/mol
Surface area35360 Å2
MethodPISA
2
C: Probable deoxyhypusine synthase
D: Probable deoxyhypusine synthase
G: Translation initiation factor 5A
H: Translation initiation factor 5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,4716
Polymers99,1444
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11500 Å2
ΔGint-56 kcal/mol
Surface area35640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.370, 136.757, 144.022
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
Probable deoxyhypusine synthase / DHS


Mass: 35060.391 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus islandicus (acidophilic) / Gene: dys, M164_1240 / Production host: Escherichia coli (E. coli) / References: UniProt: C4KGY0, deoxyhypusine synthase
#2: Protein
Translation initiation factor 5A / Hypusine-containing protein / eIF-5A


Mass: 14511.851 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus islandicus (acidophilic) / Gene: eif5a, SSO0970 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97ZE8
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.86 Å3/Da / Density % sol: 57.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 200 mM sodium trihydrate acetate pH 8.0, PEG 3360 16%, complex 7mg/ml

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.874→99.171 Å / Num. obs: 186552 / % possible obs: 48.2 % / Redundancy: 19.6 % / CC1/2: 0.999 / Net I/σ(I): 21.3
Reflection shellResolution: 1.874→1.908 Å / Num. unique obs: 4501 / CC1/2: 0.639

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.83 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2468 8519 5 %
Rwork0.1896 --
obs0.1924 170330 57.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13910 0 197 150 14257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314380
X-RAY DIFFRACTIONf_angle_d0.68219427
X-RAY DIFFRACTIONf_dihedral_angle_d7.1161926
X-RAY DIFFRACTIONf_chiral_restr0.0482205
X-RAY DIFFRACTIONf_plane_restr0.0052425
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.4382420.3039934X-RAY DIFFRACTION10
2.02-2.050.2783340.2719965X-RAY DIFFRACTION10
2.05-2.070.3103720.31091093X-RAY DIFFRACTION12
2.07-2.10.3424620.2681258X-RAY DIFFRACTION13
2.1-2.130.2612790.29251478X-RAY DIFFRACTION16
2.13-2.150.31021050.30071647X-RAY DIFFRACTION18
2.15-2.190.3186960.29341853X-RAY DIFFRACTION20
2.19-2.220.29631070.28282066X-RAY DIFFRACTION22
2.22-2.250.28761200.27222171X-RAY DIFFRACTION23
2.25-2.290.28921460.26682365X-RAY DIFFRACTION25
2.29-2.330.32381480.26242794X-RAY DIFFRACTION30
2.33-2.370.31641500.26083359X-RAY DIFFRACTION35
2.37-2.420.26061960.25454019X-RAY DIFFRACTION42
2.42-2.470.28352380.25334537X-RAY DIFFRACTION49
2.47-2.520.28723100.26685121X-RAY DIFFRACTION54
2.52-2.580.31113070.27335582X-RAY DIFFRACTION60
2.58-2.640.28433600.25566063X-RAY DIFFRACTION65
2.64-2.710.30843630.24926605X-RAY DIFFRACTION70
2.71-2.790.28973430.24067211X-RAY DIFFRACTION76
2.79-2.880.28573600.23057773X-RAY DIFFRACTION82
2.88-2.990.28484740.22378359X-RAY DIFFRACTION89
2.99-3.110.26894620.22459255X-RAY DIFFRACTION98
3.11-3.250.27185030.21629384X-RAY DIFFRACTION100
3.25-3.420.27194740.19569458X-RAY DIFFRACTION100
3.42-3.630.23615040.18529398X-RAY DIFFRACTION100
3.63-3.910.2234570.16139443X-RAY DIFFRACTION100
3.91-4.30.2225470.1469347X-RAY DIFFRACTION100
4.31-4.930.1945290.13629402X-RAY DIFFRACTION100
4.93-6.20.26574350.16419485X-RAY DIFFRACTION100
6.2-29.830.20934960.17049386X-RAY DIFFRACTION100

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