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

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Basic information

Entry
Database: PDB / ID: 1kjz
TitleStructure of the large gamma subunit of initiation factor eIF2 from Pyrococcus abyssi-G235D mutant
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
Translation initiation factor 2 subunit gamma
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR, MAD / Resolution: 1.85 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)44,9852
Polymers44,9201
Non-polymers651
Water4,864270
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.480, 86.741, 58.083
Angle α, β, γ (deg.)90.00, 110.40, 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) / Plasmid: pET3a / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.7 Å3/Da / Density % sol: 54.51 %
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: MARRESEARCH / Detector: CCD / Date: May 31, 2001
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.85→34 Å / Num. all: 40474 / Num. obs: 40474 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.9 % / Biso Wilson estimate: 30.3 Å2 / Rsym value: 0.049 / Net I/σ(I): 8
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 2309 / Rsym value: 0.324 / % possible all: 98.4
Reflection
*PLUS
Lowest resolution: 34 Å / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
% possible obs: 98.4 % / Rmerge(I) obs: 0.324

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIR, MAD / Resolution: 1.85→34 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.255 2346 RANDOM
Rwork0.225 --
all-40854 -
obs-38992 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--14 Å20 Å2-6 Å2
2--10.4 Å20 Å2
3---3.6 Å2
Refinement stepCycle: LAST / Resolution: 1.85→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3048 0 1 270 3319
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.34
LS refinement shellResolution: 1.85→1.86 Å /
RfactorNum. reflection
Rfree0.38 36
Rwork0.281 -
obs-753
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor obs: 0.225 / Rfactor Rfree: 0.255 / Rfactor Rwork: 0.225
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0051
X-RAY DIFFRACTIONc_angle_deg1.3
LS refinement shell
*PLUS
Rfactor Rfree: 0.38 / Rfactor Rwork: 0.281

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