2DY1 | pdb_00002dy1

Crystal structure of EF-G-2 from Thermus thermophilus

• PDB DOI: https://doi.org/10.2210/pdb2DY1/pdb

• Classification: SIGNALING PROTEIN, TRANSLATION
• Organism(s): Thermus thermophilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-09-04 Released: 2007-09-25 
• Deposition Author(s): Wang, H., Takemoto, C., Murayama, K., Terada, T., Chen, L., Liu, Z.J., Wang, B.C., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.204 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of EF-G-2 from Thermus thermophilus

Wang, H., Takemoto, C., Murayama, K., Terada, T., Chen, L., Liu, Z.J., Wang, B.C., Shirouzu, M., Yokoyama, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 73.78 kDa 
• Atom Count: 5,765 
• Modeled Residue Count: 660 
• Deposited Residue Count: 665 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongation factor G	A	665	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SI76 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SI76  Go to UniProtKB:  Q5SI76

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP	C [auth A]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.204 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 159.194	α = 90
b = 56.129	β = 104.568
c = 92.189	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-09-25 
Deposition Author(s): Wang, H., Takemoto, C., Murayama, K., Terada, T., Chen, L., Liu, Z.J., Wang, B.C., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-09-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description