[English] 日本語
Yorodumi
- PDB-6ozu: Crystal structure of the MIF4G domain of Trypanosoma cruzi transl... -

+
Open data


ID or keywords:

Loading...

-
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 / homology: / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlc1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more