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- PDB-5dsz: Gamma-subunit of the translation initiation factor 2 from S. solf... -

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Basic information

Entry
Database: PDB / ID: 5dsz
TitleGamma-subunit of the translation initiation factor 2 from S. solfataricus
ComponentsTranslation initiation factor 2 subunit gammaInitiation factor
KeywordsTRANSLATION / gamma-subunit / archaea / factor of initiation translation
Function / homology
Function and homology information


protein-synthesizing GTPase / formation of translation preinitiation complex / translation elongation factor activity / translation initiation factor activity / tRNA binding / GTPase activity / GTP binding / metal ion binding
Similarity search - Function
Translation initiation factor 2, gamma subunit / Initiation factor eIF2 gamma, domain 2 / Initiation factor eIF2 gamma, GTP-binding domain / Initiation factor eIF2 gamma, C-terminal / Initiation factor eIF2 gamma, C terminal / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain ...Translation initiation factor 2, gamma subunit / Initiation factor eIF2 gamma, domain 2 / Initiation factor eIF2 gamma, GTP-binding domain / Initiation factor eIF2 gamma, C-terminal / Initiation factor eIF2 gamma, C terminal / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Elongation Factor Tu (Ef-tu); domain 3 / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Translation initiation factor 2 subunit gamma
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKravchenko, O.V. / Nikonov, O.S. / Stolboushkina, E.A. / Nevskaya, N.A. / Nikulin, A.D. / Garber, M.B. / Nikonov, S.V.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
The Russian Foundation for Basic Research14-04-00571 A Russian Federation
CitationJournal: To Be Published
Title: Gamma-subunit of the translation initiation factor 2 from S. solfataricus
Authors: Kravchenko, O.V. / Nikonov, O.S. / Stolboushkina, E.A. / Nevskaya, N.A. / Nikulin, A.D. / Garber, M.B. / Nikonov, S.V.
History
DepositionSep 17, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / pdbx_data_processing_status ...diffrn_source / pdbx_data_processing_status / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jan 10, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Translation initiation factor 2 subunit gamma
B: Translation initiation factor 2 subunit gamma


Theoretical massNumber of molelcules
Total (without water)91,6982
Polymers91,6982
Non-polymers00
Water2,612145
1
A: Translation initiation factor 2 subunit gamma


Theoretical massNumber of molelcules
Total (without water)45,8491
Polymers45,8491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Translation initiation factor 2 subunit gamma


Theoretical massNumber of molelcules
Total (without water)45,8491
Polymers45,8491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.430, 95.430, 164.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Translation initiation factor 2 subunit gamma / Initiation factor / aIF2-gamma / eIF-2-gamma


Mass: 45849.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: eif2g, SSO0412 / Production host: Escherichia coli (E. coli) / References: UniProt: Q980A5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.72 Å3/Da / Density % sol: 73.93 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 15% NATRIUM MALONATE DIHYDRATE, 50MM GLYCINE, 13MM CDCL2 AT THE PROTEIN/NUCLEOTIDE MOLAR RATIO 1/10. FOR CRYOPROTECTION ETHYLENE GLYCOL WAS ADDED TO THE RESERVOIR SOLUTION AT THE FINAL CONCENTRATION OF 15% (V/V)

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Data collection

DiffractionMean temperature: 203.3 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.8148 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 19, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8148 Å / Relative weight: 1
ReflectionResolution: 2.5→23.858 Å / Num. obs: 52390 / % possible obs: 90.4 % / Redundancy: 2.85 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 7.56
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 2.84 % / Rmerge(I) obs: 0.583 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIXdev_1389refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PLF

2plf


Resolution: 2.5→23.858 Å / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.12 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2204 2640 5.04 %
Rwork0.2007 --
obs0.2018 52390 90.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→23.858 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6322 0 0 145 6467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126439
X-RAY DIFFRACTIONf_angle_d1.5678712
X-RAY DIFFRACTIONf_dihedral_angle_d14.4412428
X-RAY DIFFRACTIONf_chiral_restr0.0751021
X-RAY DIFFRACTIONf_plane_restr0.0091099
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.54550.37871490.38612831X-RAY DIFFRACTION94
2.5455-2.59440.42931500.39642849X-RAY DIFFRACTION94
2.5944-2.64730.31861530.33242908X-RAY DIFFRACTION94
2.6473-2.70470.32061490.31282825X-RAY DIFFRACTION94
2.7047-2.76760.32521520.2882887X-RAY DIFFRACTION94
2.7676-2.83670.28051520.27982897X-RAY DIFFRACTION94
2.8367-2.91320.24291510.27912851X-RAY DIFFRACTION94
2.9132-2.99880.2721510.27462875X-RAY DIFFRACTION94
2.9988-3.09540.291500.26362858X-RAY DIFFRACTION94
3.0954-3.20580.2571520.24912883X-RAY DIFFRACTION94
3.2058-3.33380.28691500.23882846X-RAY DIFFRACTION94
3.3338-3.48510.23961520.22222894X-RAY DIFFRACTION95
3.4851-3.66820.2295380.2208719X-RAY DIFFRACTION23
3.6682-3.89710.2269240.2106454X-RAY DIFFRACTION15
3.8971-4.19650.24781510.20422879X-RAY DIFFRACTION94
4.1965-4.6160.17091510.15432858X-RAY DIFFRACTION94
4.616-5.27760.15421530.1362906X-RAY DIFFRACTION95
5.2776-6.62530.18881500.16382847X-RAY DIFFRACTION94
6.6253-23.78380.16551420.14212696X-RAY DIFFRACTION88
Refinement TLS params.Method: refined / Origin x: 25.3245 Å / Origin y: -10.6471 Å / Origin z: 7.5991 Å
111213212223313233
T1.27 Å20.0079 Å20.0221 Å2-1.3575 Å2-0.0401 Å2--0.1521 Å2
L0.2663 °2-0.176 °20.3312 °2-0.093 °2-0.1928 °2--0.198 °2
S-0.068 Å °-0.32 Å °-0.0055 Å °0.0491 Å °0.0958 Å °0.1688 Å °0.367 Å °0.3614 Å °-0.0017 Å °
Refinement TLS groupSelection details: all

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