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- PDB-1yz7: Crystal structure of a C-terminal segment of the alpha subunit of... -

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Basic information

Entry
Database: PDB / ID: 1yz7
TitleCrystal structure of a C-terminal segment of the alpha subunit of aIF2 from Pyrococcus abyssi
ComponentsProbable translation initiation factor 2 alpha subunit
KeywordsTRANSLATION / helical domain / 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 / DNA polymerase; domain 1 / Alpha-Beta Plaits / Nucleic acid-binding, OB-fold / 2-Layer Sandwich / Orthogonal Bundle / 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 / MAD / Resolution: 2.26 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 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)21,7731
Polymers21,7731
Non-polymers00
Water1,17165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.538, 79.840, 47.941
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 21773.152 Da / Num. of mol.: 1 / Fragment: domains 2 and 3(residues 89-275)
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: Q9V0E4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: ammonium sulfate, isopropanol, NaCl, MOPS, pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-110.934
SYNCHROTRONESRF ID23-120.9790, 0.9756
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDMay 16, 2004
2CCD
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1crystalSINGLE WAVELENGTHMx-ray1
2crystalMADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9341
20.9791
30.97561
ReflectionResolution: 2.26→41 Å / Num. all: 11549 / Num. obs: 11549 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 10.4
Reflection shellResolution: 2.26→2.32 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 2.4 / Num. unique all: 840 / Rsym value: 0.307 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Highest resolution: 2.26 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.285 692 -random
Rwork0.236 ---
all0.239 11369 --
obs0.239 11369 98.2 %-
Displacement parametersBiso mean: 45.4 Å2
Baniso -1Baniso -2Baniso -3
1-2.431 Å20 Å20 Å2
2--5.407 Å20 Å2
3----7.838 Å2
Refinement stepCycle: LAST / Highest resolution: 2.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1423 0 0 65 1488
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0077
X-RAY DIFFRACTIONc_angle_deg1.32
LS refinement shellResolution: 2.26→2.32 Å /
RfactorNum. reflection
Rfree0.339 53
Rwork0.309 -
obs-850

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