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- PDB-4rcz: Structure of aIF2-gamma D19A variant from Sulfolobus solfataricus... -

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Basic information

Entry
Database: PDB / ID: 4rcz
TitleStructure of aIF2-gamma D19A variant 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: 1.429 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 1.2Oct 7, 2015Group: Structure summary
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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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
Water7,350408
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.400, 60.900, 143.740
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 / Mutation: D19A
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.: 408 / 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: 44.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 70% 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: 1.43→46.46 Å / Num. all: 76318 / Num. obs: 76318 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.17 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.123 / Rsym value: 0.123 / Net I/σ(I): 9.43
Reflection shellResolution: 1.43→1.52 Å / Redundancy: 6.86 % / Rmerge(I) obs: 0.752 / Mean I/σ(I) obs: 2.12 / Num. unique all: 12092 / Rsym value: 0.752 / % possible all: 99

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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 / Resolution: 1.429→46.463 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1888 3832 5.02 %RANDOM
Rwork0.1513 ---
obs0.1532 76298 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.429→46.463 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3210 0 73 408 3691
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063428
X-RAY DIFFRACTIONf_angle_d1.14677
X-RAY DIFFRACTIONf_dihedral_angle_d14.4441297
X-RAY DIFFRACTIONf_chiral_restr0.071542
X-RAY DIFFRACTIONf_plane_restr0.005586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4285-1.44660.27431310.2462592X-RAY DIFFRACTION96
1.4466-1.46570.2851150.23592646X-RAY DIFFRACTION100
1.4657-1.48570.31211400.22842644X-RAY DIFFRACTION100
1.4857-1.5070.25361320.2282651X-RAY DIFFRACTION100
1.507-1.52950.27221370.21122651X-RAY DIFFRACTION100
1.5295-1.55340.25711410.20322666X-RAY DIFFRACTION100
1.5534-1.57880.23741380.21172645X-RAY DIFFRACTION100
1.5788-1.60610.24721400.1942684X-RAY DIFFRACTION100
1.6061-1.63530.23971450.16352641X-RAY DIFFRACTION100
1.6353-1.66670.20281500.14632654X-RAY DIFFRACTION100
1.6667-1.70070.19471240.13962678X-RAY DIFFRACTION100
1.7007-1.73770.16531380.12922686X-RAY DIFFRACTION100
1.7377-1.77810.20121590.13172632X-RAY DIFFRACTION100
1.7781-1.82260.19121670.13072636X-RAY DIFFRACTION100
1.8226-1.87190.18971630.13292639X-RAY DIFFRACTION100
1.8719-1.9270.17761220.13792703X-RAY DIFFRACTION100
1.927-1.98920.21271340.13882673X-RAY DIFFRACTION100
1.9892-2.06030.17611460.13942677X-RAY DIFFRACTION100
2.0603-2.14280.18591430.1382693X-RAY DIFFRACTION100
2.1428-2.24030.15651460.13532689X-RAY DIFFRACTION100
2.2403-2.35840.19971320.13952724X-RAY DIFFRACTION100
2.3584-2.50610.1921310.14882691X-RAY DIFFRACTION100
2.5061-2.69960.1911610.15652703X-RAY DIFFRACTION100
2.6996-2.97130.18411480.1592715X-RAY DIFFRACTION100
2.9713-3.40110.18371500.14762752X-RAY DIFFRACTION100
3.4011-4.28460.17441380.13952795X-RAY DIFFRACTION100
4.2846-46.48710.17331610.16122906X-RAY DIFFRACTION100

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