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- PDB-6ozu: Crystal structure of the MIF4G domain of Trypanosoma cruzi transl... -

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Basic information

Entry
Database: PDB / ID: 6ozu
TitleCrystal structure of the MIF4G domain of Trypanosoma cruzi translation initiation factor EIF4G5
ComponentsEukaryotic translation initiation factor 4 gamma 5
KeywordsTRANSLATION / Initiation Factor / EIF4G
Function / homologyInitiation factor 4G / MIF4G domain / MIF4G-like, type 3 / translation initiation factor activity / Armadillo-type fold / RNA binding / Eukaryotic translation initiation factor 4 gamma 5 / MIF4G domain-containing protein
Function and homology information
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsGuimaraes, B.G. / Santos, L.P.C.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2019
Title: Crystal structure of the MIF4G domain of the Trypanosoma cruzi translation initiation factor EIF4G5.
Authors: Camillo Dos Santos, L.P. / de Matos, B.M. / de Maman Ribeiro, B.C. / Zanchin, N.I.T. / Guimaraes, B.G.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2019
Title: Crystal structure of the MIF4G domain of the Trypanosoma cruzi translation initiation factor EIF4G5
Authors: Santos, L.P.C. / Matos, B.M. / Ribeiro, B.C.M. / Zanchin, N.I.T. / Guimaraes, B.G.
History
DepositionMay 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 15, 2024Group: Database references / Category: citation / citation_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Eukaryotic translation initiation factor 4 gamma 5
B: Eukaryotic translation initiation factor 4 gamma 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,29921
Polymers56,4972
Non-polymers1,80119
Water1,71195
1
A: Eukaryotic translation initiation factor 4 gamma 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,19711
Polymers28,2491
Non-polymers94910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Eukaryotic translation initiation factor 4 gamma 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,10110
Polymers28,2491
Non-polymers8539
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8700 Å2
ΔGint-205 kcal/mol
Surface area20690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.100, 70.100, 303.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Eukaryotic translation initiation factor 4 gamma 5 / Putative eukaryotic translation initiation factor 4 gamma


Mass: 28248.568 Da / Num. of mol.: 2 / Fragment: residues 142-371
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: C3747_125g24, TcCL_ESM06007 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A2V2WAU2, UniProt: Q4DAD2*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.3 Å3/Da / Density % sol: 62.72 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: sodium cacodylate 0.1 M, ammonium sulfate 2 M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.051 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.051 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 30916 / % possible obs: 99.7 % / Redundancy: 12.7 % / Biso Wilson estimate: 66.66 Å2 / CC1/2: 1 / Net I/σ(I): 19.66
Reflection shellResolution: 2.4→2.54 Å / Redundancy: 13 % / Mean I/σ(I) obs: 0.94 / Num. unique obs: 62721 / CC1/2: 0.7 / % possible all: 98.4

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→48.92 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.897 / SU R Cruickshank DPI: 0.346 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.37 / SU Rfree Blow DPI: 0.253 / SU Rfree Cruickshank DPI: 0.251
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1265 5.09 %RANDOM
Rwork0.201 ---
obs0.203 24865 80.3 %-
Displacement parametersBiso max: 172.91 Å2 / Biso mean: 74.08 Å2 / Biso min: 35.06 Å2
Baniso -1Baniso -2Baniso -3
1-6.6914 Å20 Å20 Å2
2--6.6914 Å20 Å2
3----13.3827 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: final / Resolution: 2.4→48.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3789 0 101 95 3985
Biso mean--120.02 61.89 -
Num. residues----469
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1412SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes671HARMONIC5
X-RAY DIFFRACTIONt_it3953HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion496SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4558SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3953HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5342HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion2.58
X-RAY DIFFRACTIONt_other_torsion19.99
LS refinement shellResolution: 2.4→2.44 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2336 22 4.42 %
Rwork0.2672 476 -
all0.2657 498 -
obs--29.89 %
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)
11.91521.38941.1841.99850.41351.7486-0.1303-0.0428-0.0622-0.5718-0.22080.0687-0.0518-0.19990.35110.2330.11370.0678-0.2802-0.0822-0.3476-22.99625.54428.0073
22.39971.1978-2.13672.885-1.14635.6984-0.1722-0.3015-0.1776-0.2261-0.5978-0.0644-0.3868-0.32880.770.00940.12430.0331-0.0019-0.0887-0.3492-22.28560.472858.5219
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A144 - 378
2X-RAY DIFFRACTION2{ B|* }B143 - 376

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