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- PDB-1kk0: Structure of the large gamma subunit of initiation factor eIF2 fr... -

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Basic information

Entry
Database: PDB / ID: 1kk0
TitleStructure of the large gamma subunit of initiation factor eIF2 from Pyrococcus abyssi
ComponentseIF2gamma
KeywordsTRANSLATION / initiation of translation
Function / homology
Function and homology information


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, domain 2 / Initiation factor eIF2 gamma, GTP-binding domain / Initiation factor eIF2 gamma, C-terminal / 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 / Translational (tr)-type GTP-binding domain ...Translation initiation factor 2, gamma subunit / Initiation factor eIF2 gamma, domain 2 / Initiation factor eIF2 gamma, GTP-binding domain / Initiation factor eIF2 gamma, C-terminal / 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 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Elongation Factor Tu (Ef-tu); domain 3 / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 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: 1.95 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: eIF2gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3032
Polymers45,2371
Non-polymers651
Water3,567198
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.871, 86.416, 58.213
Angle α, β, γ (deg.)90.00, 109.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein eIF2gamma


Mass: 45237.121 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (archaea) / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): B834-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 / Water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.66 Å3/Da / Density % sol: 53.77 %
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: ID14-4 / Wavelength: 0.9795, 0.9797, 0.9184
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 2001
RadiationMonochromator: DIAMOND / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97971
30.91841
ReflectionResolution: 1.95→47 Å / Num. all: 34610 / Num. obs: 34217 / % possible obs: 98.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 29.1 Å2 / Rsym value: 0.04 / Net I/σ(I): 11.4
Reflection shellResolution: 1.95→2 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 2281 / Rsym value: 0.219 / % possible all: 89.4
Reflection
*PLUS
Rmerge(I) obs: 0.04
Reflection shell
*PLUS
% possible obs: 89.4 % / Rmerge(I) obs: 0.219

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIR, MAD / Resolution: 1.95→47 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.245 2013 RANDOM
Rwork0.219 --
all-34610 -
obs-33613 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--12.5 Å20 Å2-6.1 Å2
2--11.5 Å20 Å2
3---1 Å2
Refinement stepCycle: LAST / Resolution: 1.95→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3040 0 1 198 3239
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0057
X-RAY DIFFRACTIONc_angle_deg1.5
LS refinement shellResolution: 1.95→1.97 Å /
RfactorNum. reflection
Rfree0.352 51
Rwork0.312 -
obs-704
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor obs: 0.219 / Rfactor Rfree: 0.252 / Rfactor Rwork: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.352 / Rfactor Rwork: 0.312

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