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- PDB-4rd2: Structure of aIF2-gamma H97A variant from Sulfolobus solfataricus... -

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Basic information

Entry
Database: PDB / ID: 4rd2
TitleStructure of aIF2-gamma H97A variant from Sulfolobus solfataricus bound to GDPNP
ComponentsTranslation initiation factor 2 subunit gamma
KeywordsTRANSLATION / Rossmann-fold
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, 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 / FOURIER SYNTHESIS / Resolution: 1.585 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 1.1Jul 29, 2015Group: Structure summary
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Sep 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_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)46,9695
Polymers45,7821
Non-polymers1,1874
Water6,864381
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.300, 60.470, 144.290
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: 45782.160 Da / Num. of mol.: 1 / Fragment: aIF2-gamma subunit / Mutation: H97A
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.: 381 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 44.16 %
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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.58→46.34 Å / Num. all: 55647 / Num. obs: 55647 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.16 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 13.3
Reflection shellResolution: 1.58→1.68 Å / Redundancy: 7.08 % / Rmerge(I) obs: 0.816 / Mean I/σ(I) obs: 1.97 / Num. unique all: 8671 / Rsym value: 0.816 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)model building
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XDSdata scaling
PHENIX1.8.4_1496phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4RD1

4rd1


Resolution: 1.585→46.344 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2022 2822 5.07 %random
Rwork0.145 ---
obs0.1478 55644 99.41 %-
all-55647 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.585→46.344 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3208 0 73 381 3662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063430
X-RAY DIFFRACTIONf_angle_d1.0394674
X-RAY DIFFRACTIONf_dihedral_angle_d14.321306
X-RAY DIFFRACTIONf_chiral_restr0.039538
X-RAY DIFFRACTIONf_plane_restr0.005586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5845-1.61180.33321320.27822363X-RAY DIFFRACTION91
1.6118-1.64120.27731380.22732617X-RAY DIFFRACTION100
1.6412-1.67270.29421420.19442598X-RAY DIFFRACTION100
1.6727-1.70690.25031430.16932624X-RAY DIFFRACTION100
1.7069-1.7440.21741460.15592607X-RAY DIFFRACTION100
1.744-1.78460.23461280.13992655X-RAY DIFFRACTION100
1.7846-1.82920.21031430.13982598X-RAY DIFFRACTION100
1.8292-1.87860.25121510.13832609X-RAY DIFFRACTION100
1.8786-1.93390.20931390.13742633X-RAY DIFFRACTION100
1.9339-1.99630.19231580.13952614X-RAY DIFFRACTION100
1.9963-2.06770.18371310.12842628X-RAY DIFFRACTION100
2.0677-2.15050.19181290.12872648X-RAY DIFFRACTION100
2.1505-2.24840.18321240.12632678X-RAY DIFFRACTION100
2.2484-2.36690.19681440.13112640X-RAY DIFFRACTION100
2.3669-2.51520.2191500.1422656X-RAY DIFFRACTION100
2.5152-2.70930.22841410.14892666X-RAY DIFFRACTION100
2.7093-2.9820.18541250.15142679X-RAY DIFFRACTION100
2.982-3.41330.19671300.13812726X-RAY DIFFRACTION100
3.4133-4.30.17031700.13252720X-RAY DIFFRACTION100
4.3-46.36370.20431580.15762863X-RAY DIFFRACTION100

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