6U45 | pdb_00006u45

Crystal structure of Methanoperedens nitroreducens elongation factor 2 bound to GMPPCP and magnesium

• PDB DOI: https://doi.org/10.2210/pdb6U45/pdb

• Classification: TRANSLATION
• Organism(s): Candidatus Methanoperedens nitratireducens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-08-22 Released: 2020-03-18 
• Deposition Author(s): Fenwick, M.K., Ealick, S.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.224 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Structural basis of elongation factor 2 switching

Fenwick, M.K., Ealick, S.E.

(2020) Curr Res Struct Biol 2: 25-34

• DOI: https://doi.org/10.1016/j.crstbi.2020.02.001

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 162.84 kDa 
• Atom Count: 11,616 
• Modeled Residue Count: 1,429 
• Deposited Residue Count: 1,464 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongation factor 2	A, B	732	Candidatus Methanoperedens nitratireducens	Mutation(s): 0  Gene Names: fusA, ANME2D_00299
UniProt
Find proteins for A0A062V290 (Candidatus Methanoperedens nitroreducens) Explore A0A062V290  Go to UniProtKB:  A0A062V290

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GCP	C [auth A], F [auth B]	PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER C11 H18 N5 O13 P3 PHBDHXOBFUBCJD-KQYNXXCUSA-N
CL	E [auth A], H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	D [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.224 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.699	α = 90
b = 134.375	β = 90
c = 150.485	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-03-18 
Deposition Author(s): Fenwick, M.K., Ealick, S.E.

Revision History  

• Version 1.0: 2020-03-18
  Type: Initial release
  
• Version 1.1: 2024-03-13
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2024-04-03
  Changes: Refinement description