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- PDB-4rd6: Structure of aIF2-gamma from Sulfolobus solfataricus bound to GDP -

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Basic information

Entry
Database: PDB / ID: 4rd6
TitleStructure of aIF2-gamma from Sulfolobus solfataricus bound to GDP
ComponentsTranslation initiation factor 2 subunit gamma
KeywordsTRANSLATION / Rossmann fold
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
GUANOSINE-5'-DIPHOSPHATE / Translation initiation factor 2 subunit gamma
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.944 Å
AuthorsDubiez, E. / Aleksandrov, A. / Lazennec-Schurdevin, C. / Mechulam, Y. / Schmitt, E.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Identification of a second GTP-bound magnesium ion in archaeal initiation factor 2.
Authors: Dubiez, E. / Aleksandrov, A. / Lazennec-Schurdevin, C. / Mechulam, Y. / Schmitt, E.
History
DepositionSep 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 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)46,3173
Polymers45,8491
Non-polymers4682
Water6,107339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.920, 119.990, 53.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 45849.230 Da / Num. of mol.: 1 / Fragment: aIF2-gamma subunit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: eif2g, SSO0412, sulfolobus solfataricus / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 rosetta / References: UniProt: Q980A5
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.65 Å3/Da / Density % sol: 53.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 60%MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97918 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.94→48.82 Å / Num. all: 36258 / Num. obs: 36258 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.39 % / Biso Wilson estimate: 27.09 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 11.95
Reflection shellResolution: 1.94→2.06 Å / Redundancy: 4.44 % / Rmerge(I) obs: 0.755 / Mean I/σ(I) obs: 1.95 / Num. unique all: 5648 / Rsym value: 0.755 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AHO

2aho


Resolution: 1.944→48.817 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2289 1831 5.05 %random
Rwork0.1741 ---
obs0.1769 36252 98.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.944→48.817 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3140 0 29 339 3508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083297
X-RAY DIFFRACTIONf_angle_d1.14481
X-RAY DIFFRACTIONf_dihedral_angle_d15.361249
X-RAY DIFFRACTIONf_chiral_restr0.045521
X-RAY DIFFRACTIONf_plane_restr0.005566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9438-1.99640.34721230.28082467X-RAY DIFFRACTION93
1.9964-2.05510.29081370.23352627X-RAY DIFFRACTION99
2.0551-2.12150.27641580.22012576X-RAY DIFFRACTION99
2.1215-2.19730.23091490.19922560X-RAY DIFFRACTION98
2.1973-2.28530.27231460.19552619X-RAY DIFFRACTION99
2.2853-2.38930.23991200.17672696X-RAY DIFFRACTION100
2.3893-2.51520.2251280.18292664X-RAY DIFFRACTION100
2.5152-2.67280.25331550.17932662X-RAY DIFFRACTION100
2.6728-2.87910.24541290.18282650X-RAY DIFFRACTION100
2.8791-3.16880.25991490.17812671X-RAY DIFFRACTION99
3.1688-3.62720.19271500.15612667X-RAY DIFFRACTION99
3.6272-4.56940.17921550.13922698X-RAY DIFFRACTION99
4.5694-48.83270.22671320.16572864X-RAY DIFFRACTION99

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