6GFU

Crystal structure of an ancient sequence-reconstructed Elongation Factor Tu (node 262)

• PDB DOI: https://doi.org/10.2210/pdb6GFU/pdb

• Classification: TRANSLATION
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-05-02 Released: 2019-05-22 
• Deposition Author(s): Majumdar, S., Tarafder, A.D., Ge, X., Kacar, B., Sanyal, S.
• Funding Organization(s): Swedish Research Council, Wenner-Gren Foundation, Knut and Alice Wallenberg Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.233 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 

Starting Model: experimental

Literature

Crystal structure of an ancient sequence-reconstructed Elongation Factor Tu (node 262)

Majumdar, S., Tarafder, A.D., Ge, X., Kacar, B., Sanyal, S.

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)

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 44.58 kDa 
• Atom Count: 3,081 
• Modelled Residue Count: 386 
• Deposited Residue Count: 400 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongation Factor Tu	A	400	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.233 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.944	α = 90
b = 73.691	β = 90
c = 113.756	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Auto-Rickshaw	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-05-22 
Deposition Author(s): Majumdar, S., Tarafder, A.D., Ge, X., Kacar, B., Sanyal, S.

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Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	2014-4423
Swedish Research Council	Sweden	2016-06264
Wenner-Gren Foundation	Sweden	UPD 2017-0238
Knut and Alice Wallenberg Foundation	Sweden	KAW 2017.0055

Revision History  

• Version 1.0: 2019-05-22
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description