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- PDB-1yz6: Crystal structure of intact alpha subunit of aIF2 from Pyrococcus... -

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Basic information

Entry
Database: PDB / ID: 1yz6
TitleCrystal structure of intact alpha subunit of aIF2 from Pyrococcus abyssi
ComponentsProbable translation initiation factor 2 alpha subunit
KeywordsTRANSLATION / beta barrel / helical domain and alpha beta domain
Function / homology
Function and homology information


translation initiation factor activity / RNA binding
Similarity search - Function
EIF_2_alpha / Translation initiation factor 2; subunit 1; domain 2 / Translation initiation factor 2, alpha subunit, archaeal / IF2a, S1-like domain / Translation initiation factor 2, alpha subunit / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translation initiation factor 2, alpha subunit, C-terminal / Eukaryotic translation initiation factor 2 alpha subunit / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain ...EIF_2_alpha / Translation initiation factor 2; subunit 1; domain 2 / Translation initiation factor 2, alpha subunit, archaeal / IF2a, S1-like domain / Translation initiation factor 2, alpha subunit / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translation initiation factor 2, alpha subunit, C-terminal / Eukaryotic translation initiation factor 2 alpha subunit / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Nucleic acid-binding proteins / DNA polymerase; domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Alpha-Beta Plaits / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Translation initiation factor 2 subunit alpha
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.37 Å
AuthorsYatime, L. / Schmitt, E. / Blanquet, S. / Mechulam, Y.
CitationJournal: Biochemistry / Year: 2005
Title: Structure-Function Relationships of the Intact aIF2alpha Subunit from the Archaeon Pyrococcus abyssi
Authors: Yatime, L. / Schmitt, E. / Blanquet, S. / Mechulam, Y.
History
DepositionFeb 28, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 28, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable translation initiation factor 2 alpha subunit


Theoretical massNumber of molelcules
Total (without water)31,8381
Polymers31,8381
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.329, 104.329, 129.367
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Probable translation initiation factor 2 alpha subunit / eIF-2-alpha / AIF2


Mass: 31837.635 Da / Num. of mol.: 1
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 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9V0E4

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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: 5.14 Å3/Da / Density % sol: 75.7 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.6M ammonium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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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: Jun 8, 2002
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3.37→45.17 Å / Num. all: 11935 / Num. obs: 11935 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 89.7 Å2 / Rsym value: 0.058
Reflection shellResolution: 3.37→3.47 Å / Redundancy: 4.8 % / Num. unique all: 967 / Rsym value: 0.335 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Q46

1q46


Resolution: 3.37→12 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2896 592 -RANDOM
Rwork0.2495 ---
all0.272 11612 --
obs0.252 9827 84.6 %-
Displacement parametersBiso mean: 105 Å2
Baniso -1Baniso -2Baniso -3
1--20.123 Å2-17.484 Å20 Å2
2---20.123 Å20 Å2
3---40.246 Å2
Refinement stepCycle: LAST / Resolution: 3.37→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2127 0 0 0 2127
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009426
X-RAY DIFFRACTIONc_angle_deg1.49807
LS refinement shellResolution: 3.37→3.48 Å
RfactorNum. reflection% reflection
Rfree0.3838 37 -
Rwork0.3692 --
obs-643 84.6 %

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