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- PDB-1paq: CRYSTAL STRUCTURE OF THE CATALYTIC FRAGMENT OF EUKARYOTIC INITIAT... -

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Basic information

Entry
Database: PDB / ID: 1paq
TitleCRYSTAL STRUCTURE OF THE CATALYTIC FRAGMENT OF EUKARYOTIC INITIATION FACTOR 2B EPSILON
ComponentsTranslation initiation factor eIF-2B epsilon subunit
KeywordsTRANSLATION / heat repeat / aa motif
Function / homology
Function and homology information


Recycling of eIF2:GDP / eukaryotic translation initiation factor 2B complex / cytoplasmic translational initiation / guanyl-nucleotide exchange factor complex / regulation of translational initiation / translation initiation factor binding / translation initiation factor activity / guanyl-nucleotide exchange factor activity / cytosol / cytoplasm
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / Translation initiation factor eIF-2B subunit epsilon, N-terminal / Translation initiation factor eIF-2B subunit epsilon, W2 domain / eIF4-gamma/eIF5/eIF2-epsilon / Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5 / W2 domain / W2 domain profile. / Nucleotidyl transferase domain / Nucleotidyl transferase / Trimeric LpxA-like superfamily ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / Translation initiation factor eIF-2B subunit epsilon, N-terminal / Translation initiation factor eIF-2B subunit epsilon, W2 domain / eIF4-gamma/eIF5/eIF2-epsilon / Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5 / W2 domain / W2 domain profile. / Nucleotidyl transferase domain / Nucleotidyl transferase / Trimeric LpxA-like superfamily / Nucleotide-diphospho-sugar transferases / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Translation initiation factor eIF2B subunit epsilon
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsBoesen, T. / Andersen, G.R. / Pavitt, G.D.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structure of the catalytic fragment of translation initiation factor 2B and identification of a critically important catalytic residue.
Authors: Boesen, T. / Mohammad, S.S. / Pavitt, G.D. / Andersen, G.R.
History
DepositionMay 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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: Translation initiation factor eIF-2B epsilon subunit


Theoretical massNumber of molelcules
Total (without water)22,5731
Polymers22,5731
Non-polymers00
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.340, 106.340, 91.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Detailsthe monomer is the biological unit

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Components

#1: Protein Translation initiation factor eIF-2B epsilon subunit / eIF-2B GDP-GTP exchange factor / Guanine nucleotide exchange factor subunit GCD6 / GCD complex subunit GCD6


Mass: 22573.363 Da / Num. of mol.: 1 / Fragment: catalytic domain, residues (524-712)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: GCD6 OR TIF225 OR YDR211W OR YD8142.12 OR YD8142B.03 / Plasmid: pETeIF2Be-CTD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Rosetta / References: UniProt: P32501
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.87 Å3/Da / Density % sol: 57.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.75
Details: PEG 2000MME, ammonium acetate, Tris-HCl, pH 5.75, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 5 ℃ / pH: 7.4 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris-HCl1droppH7.4
25 mMdithiothreitol1drop
31 mMPMSF1drop
40.5 mMEDTA1drop
5100 mM1dropNaCl
65-8 mg/mlprotein1drop
70.2 Mammonium acetate1reservoir
823-25 %PEG2000 MME1reservoir
9100 mMsodium citrate1reservoirpH7.57

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: BW7A / Wavelength: 0.9821, 0.9824, 0.9121
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 10, 2003
RadiationMonochromator: Double crystal focussing / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.98211
20.98241
30.91211
ReflectionResolution: 2.3→20 Å / Num. all: 22335 / Num. obs: 22162 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.3→2.42 Å / % possible all: 99.2
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 20 Å / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
Highest resolution: 2.3 Å / % possible obs: 99.2 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 6.5

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2723 2111 RANDOM
Rwork0.2426 --
all0.2439 22162 -
obs0.2439 22162 -
Solvent computationBsol: 28.0924 Å2 / ksol: 0.327009 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.448 Å20 Å20 Å2
2--7.448 Å20 Å2
3----14.895 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1341 0 0 90 1431
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008266
X-RAY DIFFRACTIONc_angle_deg1.32498
X-RAY DIFFRACTIONc_mcbond_it1.0281.5
X-RAY DIFFRACTIONc_mcangle_it1.7192
X-RAY DIFFRACTIONc_scbond_it1.4422
X-RAY DIFFRACTIONc_scangle_it2.312.5
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.272 / Rfactor Rwork: 0.243
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3

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