4B44

Bacterial translation initiation factor IF2 (1-363), complex with GDP at pH8.0

• PDB DOI: https://doi.org/10.2210/pdb4B44/pdb

• Classification: TRANSLATION
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-07-27 Released: 2013-09-18 
• Deposition Author(s): Simonetti, A., Urzhumtsev, A., Klaholz, B.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.271 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Molecular Basis of GTP Hydrolysis by Bacterial Translation Initiation Factor If2

Simonetti, A., Marzi, S., Fabbretti, A., Myasnikov, A.G., Hazemann, I., Jenner, L., Urzhumtsev, A., Gualerzi, C.O., Klaholz, B.P.

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: 40.64 kDa 
• Atom Count: 2,741 
• Modelled Residue Count: 347 
• Deposited Residue Count: 363 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRANSLATION INITIATION FACTOR IF-2	A	363	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P48515 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P48515  Go to UniProtKB:  P48515

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.271 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.15	α = 90
b = 62.2	β = 90
c = 159.96	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-18 
Deposition Author(s): Simonetti, A., Urzhumtsev, A., Klaholz, B.P.

Revision History  

• Version 1.0: 2013-09-18
  Type: Initial release
  
• Version 1.1: 2015-02-11
  Changes: Structure summary
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description