3PEN | pdb_00003pen

Structure of archaeal initiation factor aIF2gamma subunit delta 37-47 from Sulfolobus solfataricus in the GDP-bound form.

• PDB DOI: https://doi.org/10.2210/pdb3PEN/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Saccharolobus solfataricus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-10-27 Released: 2011-05-04 
• Deposition Author(s): Arkhipova, V.I., Lazopulo, A.M., Lazopulo, S.M., Garber, M.B., Nikonov, O.S., Nikonov, S.V., Gabdoulkhakov, A.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.217 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Structure of archaeal initiation factor aIF2gamma subunit from Sulfolobus solfataricus in the GDP-bound form.

Arkhipova, V.I., Lazopulo, A.M., Lazopulo, S.M., Garber, M.B., Nikonov, O.S., Nikonov, S.V., Gabdoulkhakov, A.G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 45.36 kDa 
• Atom Count: 3,493 
• Modelled Residue Count: 403 
• Deposited Residue Count: 403 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Translation initiation factor 2 subunit gamma	A	403	Saccharolobus solfataricus	Mutation(s): 0  Gene Names: eif2g, SSO0412 EC: 3.6.5.3
UniProt
Find proteins for Q980A5 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q980A5  Go to UniProtKB:  Q980A5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
5GP	C [auth A]	GUANOSINE-5'-MONOPHOSPHATE C10 H14 N5 O8 P RQFCJASXJCIDSX-UUOKFMHZSA-N
MG	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.217 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 187.12	α = 90
b = 187.12	β = 90
c = 187.12	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
PHASER	phasing
PHENIX	refinement
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-04 
Deposition Author(s): Arkhipova, V.I., Lazopulo, A.M., Lazopulo, S.M., Garber, M.B., Nikonov, O.S., Nikonov, S.V., Gabdoulkhakov, A.G.

Revision History  

• Version 1.0: 2011-05-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary