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- PDB-7kcj: The crystal structure of the translation initiation factor EIF4E5... -

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Basic information

Entry
Database: PDB / ID: 7kcj
TitleThe crystal structure of the translation initiation factor EIF4E5 from Leishmania major
ComponentsEukaryotic translation initiation factor 4E type 5
KeywordsTRANSLATION
Function / homologyTranslation Initiation factor eIF- 4e / Eukaryotic initiation factor 4E / Translation Initiation factor eIF- 4e-like / eukaryotic translation initiation factor 4F complex / nuclear lumen / RNA 7-methylguanosine cap binding / ciliary plasm / translation initiation factor activity / Uncharacterized protein
Function and homology information
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.997 Å
AuthorsLima, G.B. / Guimaraes, B.G.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq) Brazil
CitationJournal: Rna Biol. / Year: 2021
Title: The translation initiation factor EIF4E5 from Leishmania: crystal structure and interacting partners.
Authors: de Lima, G.B. / de Lima Cavalcanti, T.Y.V. / de Brito, A.N.A.L.M. / de Assis, L.A. / Andrade-Vieira, R.P. / Freire, E.R. / da Silva Assuncao, T.R. / de Souza Reis, C.R. / Zanchin, N.I.T. / ...Authors: de Lima, G.B. / de Lima Cavalcanti, T.Y.V. / de Brito, A.N.A.L.M. / de Assis, L.A. / Andrade-Vieira, R.P. / Freire, E.R. / da Silva Assuncao, T.R. / de Souza Reis, C.R. / Zanchin, N.I.T. / Guimaraes, B.G. / de-Melo-Neto, O.P.
History
DepositionOct 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Eukaryotic translation initiation factor 4E type 5
B: Eukaryotic translation initiation factor 4E type 5


Theoretical massNumber of molelcules
Total (without water)50,8402
Polymers50,8402
Non-polymers00
Water3,675204
1
A: Eukaryotic translation initiation factor 4E type 5


Theoretical massNumber of molelcules
Total (without water)25,4201
Polymers25,4201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Eukaryotic translation initiation factor 4E type 5


Theoretical massNumber of molelcules
Total (without water)25,4201
Polymers25,4201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-8 kcal/mol
Surface area17010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.89, 61.89, 173.03
Angle α, β, γ (deg.)90, 90, 120
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Eukaryotic translation initiation factor 4E type 5 / EIF4E5


Mass: 25419.982 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LMJF_36_0590 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4Q217
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 1.88 Å3/Da / Density % sol: 34.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 1.25 M Sodium Citrate and 0.1 M Sodium Cacodylate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 26851 / % possible obs: 99.8 % / Redundancy: 17.5 % / Biso Wilson estimate: 38 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.1
Reflection shellResolution: 2→2.12 Å / Mean I/σ(I) obs: 0.96 / Num. unique obs: 4162 / CC1/2: 0.45

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (3-OCT-2019)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: homology model

Resolution: 1.997→46 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.936 / SU R Cruickshank DPI: 0.182 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.193 / SU Rfree Blow DPI: 0.158 / SU Rfree Cruickshank DPI: 0.154
RfactorNum. reflection% reflectionSelection details
Rfree0.2303 1343 -RANDOM
Rwork0.2011 ---
obs0.2026 26848 99.7 %-
Displacement parametersBiso mean: 41.9 Å2
Baniso -1Baniso -2Baniso -3
1-3.3556 Å20 Å20 Å2
2--3.3556 Å20 Å2
3----6.7111 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 1.997→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2807 0 0 204 3011
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082885HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.963924HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d993SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes489HARMONIC5
X-RAY DIFFRACTIONt_it2885HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion381SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2388SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.09
X-RAY DIFFRACTIONt_other_torsion16.19
LS refinement shellResolution: 2→2 Å
RfactorNum. reflection% reflection
Rfree0.247 27 -
Rwork0.247 --
obs--88.59 %
Refinement TLS params.

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)
10.3811-0.20170.17081.4537-0.45390.85520.0208-0.23810.0081-0.2381-0.00760.06290.00810.0629-0.0132-0.3273-0.00670.0038-0.31660.0037-0.2856-10.2718.7103-3.2866
21.2271-0.5667-0.38730.7129-0.11630.69150.00320.1359-0.09110.13590.0302-0.0771-0.0911-0.0771-0.0334-0.29270.00460.0151-0.33240.0275-0.2615-17.336719.39531.0822
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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