7BBN | pdb_00007bbn

Crystal structure of an ancient sequence-reconstructed Elongation Factor Tu (node 317)

• PDB DOI: https://doi.org/10.2210/pdb7BBN/pdb

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


• Deposited: 2020-12-18 Released: 2022-01-19 
• Deposition Author(s): Majumdar, S., Bergfors, T., 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: 1.68 Å
• R-Value Free: 
  0.220 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of an ancient sequence-reconstructed Elongation factor Tu (node 317)

Majumdar, S., Bergfors, T., Sanyal, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 87.18 kDa 
• Atom Count: 6,015 
• Modeled Residue Count: 727 
• Deposited Residue Count: 786 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongation Factor Tu	A, B	393	synthetic construct	Mutation(s): 0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free:  0.220 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.342	α = 90
b = 100.289	β = 90
c = 160.719	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: 2022-01-19 
Deposition Author(s): Majumdar, S., Bergfors, T., Sanyal, S.

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Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	2018-05946
Swedish Research Council	Sweden	2018-05498
Wenner-Gren Foundation	Sweden	UPD 2017-0238
Knut and Alice Wallenberg Foundation	Sweden	KAW 2017.0055

Revision History  

• Version 1.0: 2022-01-19
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description