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- PDB-1kk2: Structure of the large gamma subunit of initiation factor eIF2 fr... -

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Basic information

Entry
Database: PDB / ID: 1kk2
TitleStructure of the large gamma subunit of initiation factor eIF2 from Pyrococcus abyssi-G235D mutant complexed with GDP-Mg2+
ComponentseIF2gamma
KeywordsTRANSLATION / initiation of translation
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 / cytosol
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 / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 ...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 / Translation elongation factor EFTu-like, domain 2 / 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 speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / rigid body minimisation / Resolution: 2.1 Å
AuthorsSchmitt, E. / Blanquet, S. / Mechulam, Y.
CitationJournal: EMBO J. / Year: 2002
Title: The large subunit of initiation factor aIF2 is a close structural homologue of elongation factors.
Authors: Schmitt, E. / Blanquet, S. / Mechulam, Y.
History
DepositionDec 6, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: eIF2gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4534
Polymers44,9201
Non-polymers5333
Water3,621201
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.870, 85.660, 57.330
Angle α, β, γ (deg.)90.00, 109.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein eIF2gamma


Mass: 44920.000 Da / Num. of mol.: 1 / Mutation: G235D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (archaea) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: Q9V1G0
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.67 Å3/Da / Density % sol: 53.85 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: peg8000, tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal grow
*PLUS
pH: 6.7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
115 mg/mlprotein1drop
2200 mM1dropNaCl
310 mMMOPS1droppH6.7
410 mM2-mercaptoethanol1drop
58-18 %PEG80001reservoir
60.1 MTris-HCl1reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 1, 2001
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.1→45 Å / Num. all: 27492 / Num. obs: 27459 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Biso Wilson estimate: 30.5 Å2 / Rsym value: 0.057
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 3.8 % / Num. unique all: 2020 / Rsym value: 0.304 / % possible all: 99.6
Reflection
*PLUS
Lowest resolution: 45 Å / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 99.6 % / Rmerge(I) obs: 0.304

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Processing

Software
NameVersionClassification
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: rigid body minimisation
Starting model: 1KJZ

1kjz


Resolution: 2.1→45 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.239 1613 random
Rwork0.219 --
all-27592 -
obs-27217 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7 Å20 Å2-4.8 Å2
2--6.3 Å20 Å2
3---0.7 Å2
Refinement stepCycle: LAST / Resolution: 2.1→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3021 0 30 201 3252
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0061
X-RAY DIFFRACTIONc_angle_deg1.4
LS refinement shellResolution: 2.1→2.12 Å /
RfactorNum. reflection
Rfree0.305 53
Rwork0.293 -
obs-829
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor obs: 0.219 / Rfactor Rfree: 0.239 / Rfactor Rwork: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.305 / Rfactor Rwork: 0.293

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