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- PDB-4rd4: Structure of aIF2 gamma from sulfolobus solfataricus bound to gdpnp -

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Basic information

Entry
Database: PDB / ID: 4rd4
TitleStructure of aIF2 gamma from sulfolobus solfataricus bound to gdpnp
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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Translation initiation factor 2 subunit gamma
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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 1.0May 27, 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 1.3Oct 16, 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)47,0365
Polymers45,8491
Non-polymers1,1874
Water7,548419
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.390, 60.950, 143.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / 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: 2.21 Å3/Da / Density % sol: 44.37 %
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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97918 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2013
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.21→46.44 Å / Num. all: 120182 / Num. obs: 120182 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.45 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 10.32
Reflection shellResolution: 1.21→1.29 Å / Redundancy: 3.28 % / Rmerge(I) obs: 0.933 / Mean I/σ(I) obs: 0.92 / Num. unique all: 17761 / Rsym value: 0.933 / % possible all: 89.9

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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: 1.3→46.441 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1972 5023 5.05 %random
Rwork0.1669 ---
obs0.1684 99422 98.62 %-
all-105347 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→46.441 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3213 0 73 419 3705
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063454
X-RAY DIFFRACTIONf_angle_d1.134719
X-RAY DIFFRACTIONf_dihedral_angle_d14.4871328
X-RAY DIFFRACTIONf_chiral_restr0.072547
X-RAY DIFFRACTIONf_plane_restr0.005591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.31480.3661800.33773073X-RAY DIFFRACTION99
1.3148-1.33020.35211800.32043074X-RAY DIFFRACTION97
1.3302-1.34650.32771640.30133111X-RAY DIFFRACTION99
1.3465-1.36350.33081600.29813129X-RAY DIFFRACTION99
1.3635-1.38150.30411700.27673068X-RAY DIFFRACTION99
1.3815-1.40040.28181730.24233138X-RAY DIFFRACTION99
1.4004-1.42040.24521670.23033134X-RAY DIFFRACTION99
1.4204-1.44160.25341680.22733096X-RAY DIFFRACTION99
1.4416-1.46410.26721920.22983115X-RAY DIFFRACTION99
1.4641-1.48810.28831500.22173129X-RAY DIFFRACTION99
1.4881-1.51380.32531500.21573103X-RAY DIFFRACTION98
1.5138-1.54130.25571520.21393108X-RAY DIFFRACTION97
1.5413-1.5710.23361570.20013101X-RAY DIFFRACTION98
1.571-1.6030.23231640.18653148X-RAY DIFFRACTION98
1.603-1.63790.22631770.17443082X-RAY DIFFRACTION99
1.6379-1.6760.21621650.17093143X-RAY DIFFRACTION99
1.676-1.71790.20191690.16173136X-RAY DIFFRACTION99
1.7179-1.76440.17371460.15313128X-RAY DIFFRACTION98
1.7644-1.81630.20481650.15513139X-RAY DIFFRACTION98
1.8163-1.87490.19361760.14883123X-RAY DIFFRACTION98
1.8749-1.94190.17351480.14923162X-RAY DIFFRACTION99
1.9419-2.01970.20181770.1473188X-RAY DIFFRACTION99
2.0197-2.11160.17911420.14813199X-RAY DIFFRACTION99
2.1116-2.22290.17491800.14583145X-RAY DIFFRACTION99
2.2229-2.36220.18291760.15193191X-RAY DIFFRACTION99
2.3622-2.54460.18781650.15553187X-RAY DIFFRACTION99
2.5446-2.80060.18851800.16733165X-RAY DIFFRACTION98
2.8006-3.20580.17421670.1583243X-RAY DIFFRACTION99
3.2058-4.03860.16591710.14833279X-RAY DIFFRACTION99
4.0386-46.4710.19341920.16833362X-RAY DIFFRACTION98

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