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- PDB-4m2l: Gamma subunit of the translation initiation factor 2 from Sulfolo... -

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Basic information

Entry
Database: PDB / ID: 4m2l
TitleGamma subunit of the translation initiation factor 2 from Sulfolobus solfataricus in nucleotide-free form
ComponentsTranslation initiation factor 2 subunit gamma
KeywordsTRANSLATION / aIF2 / aIF2 gamma subunit / G-protein / translation initiation / protein biosynthesis / RNA-binding / GTP-binding / nucleotide-binding
Function / homology
Function and homology information


formation of translation preinitiation complex / protein-synthesizing GTPase / 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, C-terminal / Initiation factor eIF2 gamma, domain 2 / Initiation factor eIF2 gamma, GTP-binding domain / Initiation factor eIF2 gamma, C terminal / : / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors / Elongation factor Tu domain 2 / Elongation Factor Tu (Ef-tu); domain 3 ...Translation initiation factor 2, gamma subunit / Initiation factor eIF2 gamma, C-terminal / Initiation factor eIF2 gamma, domain 2 / Initiation factor eIF2 gamma, GTP-binding domain / Initiation factor eIF2 gamma, C terminal / : / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors / Elongation factor Tu domain 2 / Elongation Factor Tu (Ef-tu); domain 3 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Translation initiation factor 2 subunit gamma
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.149 Å
AuthorsNikonov, O.S. / Stolboushkina, E.A. / Arkhipova, V.I. / Gabdulkhakov, A.G. / Nikulin, A.D. / Garber, M.B. / Nikonov, S.V.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Conformational transitions in the gamma subunit of the archaeal translation initiation factor 2.
Authors: Nikonov, O. / Stolboushkina, E. / Arkhipova, V. / Kravchenko, O. / Nikonov, S. / Garber, M.
History
DepositionAug 5, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Category: citation / struct_ref_seq_dif
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Translation initiation factor 2 subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,70136
Polymers45,2611
Non-polymers2,44035
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.815, 95.815, 165.240
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-647-

HOH

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Components

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


Mass: 45261.453 Da / Num. of mol.: 1 / Mutation: 41-45 Deletion mutant
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: eif2g / Production host: Escherichia coli (E. coli) / References: UniProt: Q980A5
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.84 Å3/Da / Density % sol: 74.57 %
Crystal growTemperature: 301 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25mM Tris-HCl, 400mM NaCl, 10mM 2-mercaptoethanol, 25mM Na-HEPES, 25mM MgSO4, 0.8M Li2SO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 301K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 4, 2012
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.149→82.99 Å / Num. all: 48518 / Num. obs: 48518 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.86 % / Biso Wilson estimate: 40.41 Å2 / Rmerge(I) obs: 0.0568 / Net I/σ(I): 18.01
Reflection shellResolution: 2.15→2.25 Å / Redundancy: 5.87 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 3.83 / Num. unique all: 6088 / % possible all: 99.7

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AHO

2aho


Resolution: 2.149→47.908 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.21 / σ(F): 2 / Phase error: 24.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2282 2410 5.06 %RANDOM
Rwork0.1884 ---
all0.1922 48428 --
obs0.1904 47620 98.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.4 Å2 / Biso mean: 42.5425 Å2 / Biso min: 17.06 Å2
Refinement stepCycle: LAST / Resolution: 2.149→47.908 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3080 0 148 255 3483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073248
X-RAY DIFFRACTIONf_angle_d1.1274346
X-RAY DIFFRACTIONf_chiral_restr0.076502
X-RAY DIFFRACTIONf_plane_restr0.006536
X-RAY DIFFRACTIONf_dihedral_angle_d16.5631209
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1491-2.19290.31121340.25752549268396
2.1929-2.24060.26691590.23262567272697
2.2406-2.29270.25141170.21342595271297
2.2927-2.35010.28141390.21952593273297
2.3501-2.41360.2721550.20192574272997
2.4136-2.48460.24831300.20912620275098
2.4846-2.56480.27511330.20512635276898
2.5648-2.65650.23891310.20212660279198
2.6565-2.76280.2631320.20612643277598
2.7628-2.88860.28891480.21292637278598
2.8886-3.04080.23721440.20152658280299
3.0408-3.23130.22331370.19032688282599
3.2313-3.48070.22481540.18912684283899
3.4807-3.83090.19171520.17142731288399
3.8309-4.38490.18621220.155527372859100
4.3849-5.52320.1741630.1627422905100
5.5232-47.91940.27371600.204928973057100

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